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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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2
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Cole AG, Kultgen SG, Mani N, Quintero JG, Yi Fan K, Ardzinski A, Stever K, Dorsey BD, Phelps JR, Lee ACH, Thi EP, Chiu T, Tang S, Horanyi PS, Mayclin SJ, Harasym TO, Sofia MJ. Design, synthesis, and structure-activity relationship of a bicyclic HBV capsid assembly modulator chemotype leading to the identification of clinical candidate AB-506. Bioorg Med Chem Lett 2023; 94:129456. [PMID: 37633618 DOI: 10.1016/j.bmcl.2023.129456] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 08/28/2023]
Abstract
Disruption of the HBV capsid assembly process through small-molecule interaction with HBV core protein is a validated target for the suppression of hepatitis B viral replication and the development of new antivirals. Through combination of key structural features associated with two distinct series of capsid assembly modulators, a novel aminochroman-based chemotype was identified. Optimization of anti-HBV potency through generation of SAR in addition to further core modifications provided a series of related functionalized aminoindanes. Key compounds demonstrated excellent cellular potency in addition to favorable ADME and pharmacokinetic profiles and were shown to be highly efficacious in a mouse model of HBV replication. Aminoindane derivative AB-506 was subsequently advanced into clinical development.
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Affiliation(s)
- Andrew G Cole
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA.
| | - Steven G Kultgen
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Nagraj Mani
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Jorge G Quintero
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Kristi Yi Fan
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Andrzej Ardzinski
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Kim Stever
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Bruce D Dorsey
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Janet R Phelps
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Amy C H Lee
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Emily P Thi
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Tim Chiu
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Sunny Tang
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Peter S Horanyi
- UCB Pharma, 87 Cambridge Park Drive, Cambridge, MA 02140, USA
| | | | - Troy O Harasym
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
| | - Michael J Sofia
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, PA 18974, USA
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3
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Moorefield J, Konuk Y, Norman JO, Abendroth J, Edwards TE, Lorimer DD, Mayclin SJ, Staker BL, Craig JK, Barett KF, Barrett LK, Van Voorhis WC, Myler PJ, McLaughlin KJ. Characterization of a family I inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1. Acta Crystallogr F Struct Biol Commun 2023; 79:257-266. [PMID: 37728609 PMCID: PMC10565794 DOI: 10.1107/s2053230x23008002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/13/2023] [Indexed: 09/21/2023] Open
Abstract
Inorganic pyrophosphate (PPi) is generated as an intermediate or byproduct of many fundamental metabolic pathways, including DNA/RNA synthesis. The intracellular concentration of PPi must be regulated as buildup can inhibit many critical cellular processes. Inorganic pyrophosphatases (PPases) hydrolyze PPi into two orthophosphates (Pi), preventing the toxic accumulation of the PPi byproduct in cells and making Pi available for use in biosynthetic pathways. Here, the crystal structure of a family I inorganic pyrophosphatase from Legionella pneumophila is reported at 2.0 Å resolution. L. pneumophila PPase (LpPPase) adopts a homohexameric assembly and shares the oligonucleotide/oligosaccharide-binding (OB) β-barrel core fold common to many other bacterial family I PPases. LpPPase demonstrated hydrolytic activity against a general substrate, with Mg2+ being the preferred metal cofactor for catalysis. Legionnaires' disease is a severe respiratory infection caused primarily by L. pneumophila, and thus increased characterization of the L. pneumophila proteome is of interest.
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Affiliation(s)
- Julia Moorefield
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Yagmur Konuk
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Jordan O. Norman
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Stephen J. Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Justin K. Craig
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Kayleigh F. Barett
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lynn K. Barrett
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Krystle J. McLaughlin
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
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4
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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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5
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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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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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8
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Riboldi GP, Zigweid R, Myler PJ, Mayclin SJ, Couñago RM, Staker BL. Identification of P218 as a potent inhibitor of Mycobacterium ulcerans DHFR. RSC Med Chem 2021; 12:103-109. [PMID: 34046602 PMCID: PMC8130613 DOI: 10.1039/d0md00303d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/07/2020] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium ulcerans is the causative agent of Buruli ulcer, a debilitating chronic disease that mainly affects the skin. Current treatments for Buruli ulcer are efficacious, but rely on the use of antibiotics with severe side effects. The enzyme dihydrofolate reductase (DHFR) plays a critical role in the de novo biosynthesis of folate species and is a validated target for several antimicrobials. Here we describe the biochemical and structural characterization of M. ulcerans DHFR and identified P218, a safe antifolate compound in clinical evaluation for malaria, as a potent inhibitor of this enzyme. We expect our results to advance M. ulcerans DHFR as a target for future structure-based drug discovery campaigns.
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Affiliation(s)
- Gustavo P Riboldi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP) Campinas SP 13083-875 Brazil
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP Campinas SP 13083-886 Brazil
| | - Rachael Zigweid
- Center for Infectious Disease Research, Seattle Children's Research Institute Seattle Washington 98109 USA
| | - Peter J Myler
- Center for Infectious Disease Research, Seattle Children's Research Institute Seattle Washington 98109 USA
- Department of Pediatrics, University of Washington Seattle Washington 91895 USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID) Seattle Washington 98109 USA
- UCB Bainbridge Island Washington 98110 USA
| | - Rafael M Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP) Campinas SP 13083-875 Brazil
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP Campinas SP 13083-886 Brazil
| | - Bart L Staker
- Center for Infectious Disease Research, Seattle Children's Research Institute Seattle Washington 98109 USA
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Patel SM, Smith TG, Morton M, Stiers KM, Seravalli J, Mayclin SJ, Edwards TE, Tanner JJ, Becker DF. Cautionary Tale of Using Tris(alkyl)phosphine Reducing Agents with NAD +-Dependent Enzymes. Biochemistry 2020; 59:3285-3289. [PMID: 32841567 DOI: 10.1021/acs.biochem.0c00490] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein biochemistry protocols typically include disulfide bond reducing agents to guard against unwanted thiol oxidation and protein aggregation. Commonly used disulfide bond reducing agents include dithiothreitol, β-mercaptoethanol, glutathione, and the tris(alkyl)phosphine compounds tris(2-carboxyethyl)phosphine (TCEP) and tris(3-hydroxypropyl)phosphine (THPP). While studying the catalytic activity of the NAD(P)H-dependent enzyme Δ1-pyrroline-5-carboxylate reductase, we unexpectedly observed a rapid non-enzymatic chemical reaction between NAD+ and the reducing agents TCEP and THPP. The product of the reaction exhibits a maximum ultraviolet absorbance peak at 334 nm and forms with an apparent association rate constant of 231-491 M-1 s-1. The reaction is reversible, and nuclear magnetic resonance characterization (1H, 13C, and 31P) of the product revealed a covalent adduct between the phosphorus of the tris(alkyl)phosphine reducing agent and the C4 atom of the nicotinamide ring of NAD+. We also report a 1.45 Å resolution crystal structure of short-chain dehydrogenase/reductase with the NADP+-TCEP reaction product bound in the cofactor binding site, which shows that the adduct can potentially inhibit enzymes. These findings serve to caution researchers when using TCEP or THPP in experimental protocols with NAD(P)+. Because NAD(P)+-dependent oxidoreductases are widespread in nature, our results may be broadly relevant.
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Affiliation(s)
| | | | | | - Kyle M Stiers
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | | | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease, UCB Pharma, Bainbridge Island, Washington 98110, United States
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, UCB Pharma, Bainbridge Island, Washington 98110, United States
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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Lerch TF, Sharpe P, Mayclin SJ, Edwards TE, Lee E, Conlon HD, Polleck S, Rouse JC, Luo Y, Zou Q. Infliximab crystal structures reveal insights into self-association. MAbs 2017; 9:874-883. [PMID: 28421849 DOI: 10.1080/19420862.2017.1320463] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Aggregation and self-association in protein-based biotherapeutics are critical quality attributes that are tightly controlled by the manufacturing process. Aggregates have the potential to elicit immune reactions, including neutralizing anti-drug antibodies, which can diminish the drug's efficacy upon subsequent dosing. The structural basis of reversible self-association, a form of non-covalent aggregation in the native state, is only beginning to emerge for many biologics and is often unique to a given molecule. In the present study, crystal structures of the infliximab (Remicade) Fc and Fab domains were determined. The Fab domain structures are the first to be reported in the absence of the antigen (i.e., tumor necrosis factor), and are consistent with a mostly rigid complementarity-determining region loop structure and rotational flexibility between variable and constant regions. A potential self-association interface is conserved in two distinct crystal forms of the Fab domain, and solution studies further demonstrate that reversible self-association of infliximab is mediated by the Fab domain. The crystal structures and corresponding solution studies help rationalize the propensity for infliximab to self-associate and provide insights for the design of improved control strategies in biotherapeutics development.
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Affiliation(s)
- Thomas F Lerch
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc. , Chesterfield , MO , USA
| | - Penelope Sharpe
- b Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc. , Andover , MA , USA
| | | | | | - Eunhee Lee
- b Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc. , Andover , MA , USA
| | - Hugh D Conlon
- b Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc. , Andover , MA , USA
| | - Sharon Polleck
- b Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc. , Andover , MA , USA
| | - Jason C Rouse
- b Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc. , Andover , MA , USA
| | - Yin Luo
- b Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc. , Andover , MA , USA
| | - Qin Zou
- a Analytical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc. , Chesterfield , MO , USA
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11
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Haft DH, Pierce PG, Mayclin SJ, Sullivan A, Gardberg AS, Abendroth J, Begley DW, Phan IQ, Staker BL, Myler PJ, Marathias VM, Lorimer DD, Edwards TE. Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors. Sci Rep 2017; 7:41074. [PMID: 28120876 PMCID: PMC5264612 DOI: 10.1038/srep41074] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/12/2016] [Indexed: 01/08/2023] Open
Abstract
During human infection, Mycobacterium tuberculosis (Mtb) survives the normally bacteriocidal phagosome of macrophages. Mtb and related species may be able to combat this harsh acidic environment which contains reactive oxygen species due to the mycobacterial genomes encoding a large number of dehydrogenases. Typically, dehydrogenase cofactor binding sites are open to solvent, which allows NAD/NADH exchange to support multiple turnover. Interestingly, mycobacterial short chain dehydrogenases/reductases (SDRs) within family TIGR03971 contain an insertion at the NAD binding site. Here we present crystal structures of 9 mycobacterial SDRs in which the insertion buries the NAD cofactor except for a small portion of the nicotinamide ring. Line broadening and STD-NMR experiments did not show NAD or NADH exchange on the NMR timescale. STD-NMR demonstrated binding of the potential substrate carveol, the potential product carvone, the inhibitor tricyclazol, and an external redox partner 2,6-dichloroindophenol (DCIP). Therefore, these SDRs appear to contain a non-exchangeable NAD cofactor and may rely on an external redox partner, rather than cofactor exchange, for multiple turnover. Incidentally, these genes always appear in conjunction with the mftA gene, which encodes the short peptide MftA, and with other genes proposed to convert MftA into the external redox partner mycofactocin.
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Affiliation(s)
- Daniel H Haft
- National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Phillip G Pierce
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Amy Sullivan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Anna S Gardberg
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA.,University of Washington, Department of Medical Education and Biomedical Informatics &Department of Global Health, Seattle WA 98195, USA
| | - Vasilios M Marathias
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
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