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Roszczenko-Jasińska P, Giełdoń A, Mazur D, Spodzieja M, Plichta M, Czaplewski C, Bal W, Jagusztyn-Krynicka EK, Bartosik D. Exploring the inhibitory potential of in silico-designed small peptides on Helicobacter pylori Hp0231 (DsbK), a periplasmic oxidoreductase involved in disulfide bond formation. Front Mol Biosci 2024; 10:1335704. [PMID: 38274095 PMCID: PMC10810133 DOI: 10.3389/fmolb.2023.1335704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction: Helicobacter pylori is a bacterium that colonizes the gastric epithelium, which affects millions of people worldwide. H. pylori infection can lead to various gastrointestinal diseases, including gastric adenocarcinoma and mucosa-associated lymphoid tissue lymphoma. Conventional antibiotic therapies face challenges due to increasing antibiotic resistance and patient non-compliance, necessitating the exploration of alternative treatment approaches. In this study, we focused on Hp0231 (DsbK), an essential component of the H. pylori Dsb (disulfide bond) oxidative pathway, and investigated peptide-based inhibition as a potential therapeutic strategy. Methods: Three inhibitory peptides designed by computational modeling were evaluated for their effectiveness using a time-resolved fluorescence assay. We also examined the binding affinity between Hp0231 and the peptides using microscale thermophoresis. Results and discussion: Our findings demonstrate that in silico-designed synthetic peptides can effectively inhibit Hp0231-mediated peptide oxidation. Targeting Hp0231 oxidase activity could attenuate H. pylori virulence without compromising bacterial viability. Therefore, peptide-based inhibitors of Hp0231 could be candidates for the development of new targeted strategy, which does not influence the composition of the natural human microbiome, but deprive the bacterium of its pathogenic properties.
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Affiliation(s)
- Paula Roszczenko-Jasińska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Dominika Mazur
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | - Maciej Plichta
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Lu SH, Liang XN, Nong XJ, Chen R, Li XX. A New HPLC-UV Method Using Hydrolyzation with Sodium Hydroxide for Quantitation of Trans- p-Hydroxycinnamic Acid and Total Trans- p-Hydroxycinnamic Acid Esters in the Leaves of Ligustrum robustum. Molecules 2023; 28:5309. [PMID: 37513183 PMCID: PMC10383156 DOI: 10.3390/molecules28145309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Trans-p-hydroxycinnamic acid and its esters in the leaves of Ligustrum robustum might be a new resource to prevent diabetes and its complications. In the present study, a new HPLC-UV method using hydrolyzation with sodium hydroxide for quantitation of trans-p-hydroxycinnamic acid and total trans-p-hydroxycinnamic acid esters in the leaves of L. robustum was developed, since it was difficult and troublesome to analyze no less than 34 trans-p-hydroxycinnamic acid esters by usual HPLC. The extract of L. robustum was hydrolyzed with sodium hydroxide at 80 °C for 2 h, and then, hydrochloride was added. HPLC analysis was performed in reverse phase mode using a C-18 column, eluting with methanol-0.1% acetic acid aqueous solution (40:60, v/v) in isocratic mode at a flow rate of 1.0 mL·min-1 and detecting at 310 nm. The linear range for trans-p-hydroxycinnamic acid was 11.0-352.0 μg·mL-1 (r2 = 1.000). The limit of detection and limit of quantification were 2.00 and 6.07 μg·mL-1, respectively. The relative standard deviations of intra-day and inter-day variabilities for trans-p-hydroxycinnamic acid were less than 2%. The percentage recovery of trans-p-hydroxycinnamic acid was 103.3% ± 1.1%. It is the first HPLC method using hydrolyzation for quantification of many carboxylic esters. Finally, the method was used successfully to determine trans-p-hydroxycinnamic acid and total trans-p-hydroxycinnamic acid esters in various extracts of the leaves of L. robustum. The 60-70% ethanol extracts of L. robustum showed the highest contents of free trans-p-hydroxycinnamic acid (3.96-3.99 mg·g-1), and the 50-80% ethanol extracts of L. robustum displayed the highest contents of total trans-p-hydroxycinnamic acid esters (202.6-210.6 mg·g-1). The method can be applied also to the quality control of the products of L. robustum.
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Affiliation(s)
- Shi-Hui Lu
- College of Pharmacy, Youjiang Medical University for Nationalities, Baise 533000, China
- Guangxi Database Construction and Application Engineering Research Center for in Tracorporal Pharmacochemistry of TCM, Baise 533000, China
- Key Laboratory of Youjiang Basin Characteristic Ethnic Medicine Research in Guangxi, Baise 533000, China
| | - Xiao-Na Liang
- College of Pharmacy, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Xiao-Jin Nong
- College of Pharmacy, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Ran Chen
- Institute of Life Science, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Xiu-Xia Li
- Nursing School, Youjiang Medical University for Nationalities, Baise 533000, China
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3
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Fragment-Based Lead Discovery Strategies in Antimicrobial Drug Discovery. Antibiotics (Basel) 2023; 12:antibiotics12020315. [PMID: 36830226 PMCID: PMC9951956 DOI: 10.3390/antibiotics12020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Fragment-based lead discovery (FBLD) is a powerful application for developing ligands as modulators of disease targets. This approach strategy involves identification of interactions between low-molecular weight compounds (100-300 Da) and their putative targets, often with low affinity (KD ~0.1-1 mM) interactions. The focus of this screening methodology is to optimize and streamline identification of fragments with higher ligand efficiency (LE) than typical high-throughput screening. The focus of this review is on the last half decade of fragment-based drug discovery strategies that have been used for antimicrobial drug discovery.
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Whitehouse RL, Alwan WS, Ilyichova OV, Taylor AJ, Chandrashekaran IR, Mohanty B, Doak BC, Scanlon MJ. Fragment screening libraries for the identification of protein hot spots and their minimal binding pharmacophores. RSC Med Chem 2023; 14:135-143. [PMID: 36760747 PMCID: PMC9890547 DOI: 10.1039/d2md00253a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/11/2022] [Indexed: 11/30/2022] Open
Abstract
Fragment-based drug design relies heavily on structural information for the elaboration and optimisation of hits. The ability to identify neighbouring binding hot spots, energetically favourable interactions and conserved binding motifs in protein structures through X-ray crystallography can inform the evolution of fragments into lead-like compounds through structure-based design. The composition of fragment libraries can be designed and curated to fit this purpose and herein, we describe and compare screening libraries containing compounds comprising between 2 and 18 heavy atoms. We evaluate the properties of the compounds in these libraries and assess their ability to probe protein surfaces for binding hot spots.
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Affiliation(s)
- Rebecca L Whitehouse
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Wesam S Alwan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Olga V Ilyichova
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- Australian Synchrotron, ANSTO Clayton VIC 3168 Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Ashley J Taylor
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Indu R Chandrashekaran
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Bradley C Doak
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
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Wang G, Mohanty B, Williams ML, Doak BC, Dhouib R, Totsika M, McMahon R, Sharma G, Zheng D, Bentley MR, Chin YKY, Horne J, Chalmers DK, Heras B, Scanlon MJ. Selective binding of small molecules to Vibrio cholerae DsbA offers a starting point for the design of novel antibacterials. ChemMedChem 2022; 17:e202100673. [PMID: 34978144 PMCID: PMC9305425 DOI: 10.1002/cmdc.202100673] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/23/2021] [Indexed: 11/25/2022]
Abstract
DsbA enzymes catalyze oxidative folding of proteins that are secreted into the periplasm of Gram‐negative bacteria, and they are indispensable for the virulence of human pathogens such as Vibrio cholerae and Escherichia coli. Therefore, targeting DsbA represents an attractive approach to control bacterial virulence. X‐ray crystal structures reveal that DsbA enzymes share a similar fold, however, the hydrophobic groove adjacent to the active site, which is implicated in substrate binding, is shorter and flatter in the structure of V. cholerae DsbA (VcDsbA) compared to E. coli DsbA (EcDsbA). The flat and largely featureless nature of this hydrophobic groove is challenging for the development of small molecule inhibitors. Using fragment‐based screening approaches, we have identified a novel small molecule, based on the benzimidazole scaffold, that binds to the hydrophobic groove of oxidized VcDsbA with a KD of 446±10 μM. The same benzimidazole compound has ∼8‐fold selectivity for VcDsbA over EcDsbA and binds to oxidized EcDsbA, with KD>3.5 mM. We generated a model of the benzimidazole complex with VcDsbA using NMR data but were unable to determine the structure of the benzimidazole bound EcDsbA using either NMR or X‐ray crystallography. Therefore, a structural basis for the observed selectivity is unclear. To better understand ligand binding to these two enzymes we crystallized each of them in complex with a known ligand, the bile salt sodium taurocholate. The crystal structures show that taurocholate adopts different binding poses in complex with VcDsbA and EcDsbA, and reveal the protein‐ligand interactions that stabilize the different modes of binding. This work highlights the capacity of fragment‐based drug discovery to identify inhibitors of challenging protein targets. In addition, it provides a starting point for development of more potent and specific VcDsbA inhibitors that act through a novel anti‐virulence mechanism.
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Affiliation(s)
- Geqing Wang
- La Trobe University - Bundoora Campus: La Trobe University, Department of Biochemistry and Genetics, AUSTRALIA
| | | | - Martin L Williams
- Monash Institute of Pharmaceutical Sciences, Medicinal Chemistry, AUSTRALIA
| | - Bradley C Doak
- Monash Institute of Pharmaceutical Sciences, Medicinal Chemistry, AUSTRALIA
| | - Rabeb Dhouib
- Queensland University of Technology, School of Biomedical Sciences, AUSTRALIA
| | - Makrina Totsika
- Queensland University of Technology, School of Biomedical Sciences, AUSTRALIA
| | - Roisin McMahon
- Griffith University, Griffith Institute for Drug Discovery, AUSTRALIA
| | - Gaurav Sharma
- Monash Institute of Pharmaceutical Sciences, Medicinal Chemistry, AUSTRALIA
| | - Dan Zheng
- Monash Institute of Pharmaceutical Sciences, Medicinal Chemistry, AUSTRALIA
| | - Matthew R Bentley
- Monash Institute of Pharmaceutical Sciences, Medicinal Chemistry, AUSTRALIA
| | - Yanni Ka-Yan Chin
- The University of Queensland, Cantre for Advanced Imaging, AUSTRALIA
| | - James Horne
- University of Tasmania, Central Science Laboratory, AUSTRALIA
| | - David K Chalmers
- Monash Institute of Pharmaceutical Sciences, Medicinal Chemistry, AUSTRALIA
| | - Begoña Heras
- La Trobe University, Department of Biochemistry and Genetics, AUSTRALIA
| | - Martin Joseph Scanlon
- Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, Medicinal Chemistry, 381 Royal Parade, Monash University, 3052, Parkville, AUSTRALIA
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Petit GA, Mohanty B, McMahon RM, Nebl S, Hilko DH, Wilde KL, Scanlon MJ, Martin JL, Halili MA. Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket of Burkholderia pseudomallei DsbA. Acta Crystallogr D Struct Biol 2022; 78:75-90. [PMID: 34981764 PMCID: PMC8725163 DOI: 10.1107/s2059798321011475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/29/2021] [Indexed: 01/10/2023] Open
Abstract
Disulfide-bond-forming proteins (Dsbs) play a crucial role in the pathogenicity of many Gram-negative bacteria. Disulfide-bond-forming protein A (DsbA) catalyzes the formation of the disulfide bonds necessary for the activity and stability of multiple substrate proteins, including many virulence factors. Hence, DsbA is an attractive target for the development of new drugs to combat bacterial infections. Here, two fragments, bromophenoxy propanamide (1) and 4-methoxy-N-phenylbenzenesulfonamide (2), were identified that bind to DsbA from the pathogenic bacterium Burkholderia pseudomallei, the causative agent of melioidosis. The crystal structures of oxidized B. pseudomallei DsbA (termed BpsDsbA) co-crystallized with 1 or 2 show that both fragments bind to a hydrophobic pocket that is formed by a change in the side-chain orientation of Tyr110. This conformational change opens a `cryptic' pocket that is not evident in the apoprotein structure. This binding location was supported by 2D-NMR studies, which identified a chemical shift perturbation of the Tyr110 backbone amide resonance of more than 0.05 p.p.m. upon the addition of 2 mM fragment 1 and of more than 0.04 p.p.m. upon the addition of 1 mM fragment 2. Although binding was detected by both X-ray crystallography and NMR, the binding affinity (Kd) for both fragments was low (above 2 mM), suggesting weak interactions with BpsDsbA. This conclusion is also supported by the crystal structure models, which ascribe partial occupancy to the ligands in the cryptic binding pocket. Small fragments such as 1 and 2 are not expected to have a high energetic binding affinity due to their relatively small surface area and the few functional groups that are available for intermolecular interactions. However, their simplicity makes them ideal for functionalization and optimization. The identification of the binding sites of 1 and 2 to BpsDsbA could provide a starting point for the development of more potent novel antimicrobial compounds that target DsbA and bacterial virulence.
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Affiliation(s)
- Guillaume A. Petit
- Griffith Institute for Drug Discovery, Griffith University, Building N75, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Sydney Analytical Core Research Facility, The University of Sydney, Sydney, NSW 2006, Australia
| | - Róisín M. McMahon
- Griffith Institute for Drug Discovery, Griffith University, Building N75, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Stefan Nebl
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - David H. Hilko
- Griffith Institute for Drug Discovery, Griffith University, Building N75, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Karyn L. Wilde
- National Deuteration Facility, Australian Nuclear Science and Technology Organization (ANSTO), New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Martin J. Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Jennifer L. Martin
- Griffith Institute for Drug Discovery, Griffith University, Building N75, 46 Don Young Road, Nathan, QLD 4111, Australia
- Vice-Chancellor’s Unit, University of Wollongong, Building 36, Wollongong, NSW 2522, Australia
| | - Maria A. Halili
- Griffith Institute for Drug Discovery, Griffith University, Building N75, 46 Don Young Road, Nathan, QLD 4111, Australia
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Santos-Martin C, Wang G, Subedi P, Hor L, Totsika M, Paxman JJ, Heras B. Structural bioinformatic analysis of DsbA proteins and their pathogenicity associated substrates. Comput Struct Biotechnol J 2021; 19:4725-4737. [PMID: 34504665 PMCID: PMC8405906 DOI: 10.1016/j.csbj.2021.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 01/02/2023] Open
Abstract
The disulfide bond (DSB) forming system and in particular DsbA, is a key bacterial oxidative folding catalyst. Due to its role in promoting the correct assembly of a wide range of virulence factors required at different stages of the infection process, DsbA is a master virulence rheostat, making it an attractive target for the development of new virulence blockers. Although DSB systems have been extensively studied across different bacterial species, to date, little is known about how DsbA oxidoreductases are able to recognize and interact with such a wide range of substrates. This review summarizes the current knowledge on the DsbA enzymes, with special attention on their interaction with the partner oxidase DsbB and substrates associated with bacterial virulence. The structurally and functionally diverse set of bacterial proteins that rely on DsbA-mediated disulfide bond formation are summarized. Local sequence and secondary structure elements of these substrates are analyzed to identify common elements recognized by DsbA enzymes. This not only provides information on protein folding systems in bacteria but also offers tools for identifying new DsbA substrates and informs current efforts aimed at developing DsbA targeted anti-microbials.
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Affiliation(s)
- Carlos Santos-Martin
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Australia
| | - Geqing Wang
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Australia
| | - Pramod Subedi
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Australia
| | - Lilian Hor
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Jason John Paxman
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, Australia
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Elaboration of a benzofuran scaffold and evaluation of binding affinity and inhibition of Escherichia coli DsbA: A fragment-based drug design approach to novel antivirulence compounds. Bioorg Med Chem 2021; 45:116315. [PMID: 34364222 DOI: 10.1016/j.bmc.2021.116315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/20/2022]
Abstract
Bacterial thiol-disulfide oxidoreductase DsbA is essential for bacterial virulence factor assembly and has been identified as a viable antivirulence target. Herein, we report a structure-based elaboration of a benzofuran hit that bound to the active site groove of Escherichia coli DsbA. Substituted phenyl groups were installed at the 5- and 6-position of the benzofuran using Suzuki-Miyaura coupling. HSQC NMR titration experiments showed dissociation constants of this series in the high µM to low mM range and X-ray crystallography produced three co-structures, showing binding in the hydrophobic groove, comparable with that of the previously reported benzofurans. The 6-(m-methoxy)phenyl analogue (2b), which showed a promising binding pose, was chosen for elaboration from the C-2 position. The 2,6-disubstituted analogues bound to the hydrophobic region of the binding groove and the C-2 groups extended into the more polar, previously un-probed, region of the binding groove. Biochemical analysis of the 2,6-disubsituted analogues showed they inhibited DsbA oxidation activity in vitro. The results indicate the potential to develop the elaborated benzofuran series into a novel class of antivirulence compounds.
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Lim KYL, Mullally CA, Haese EC, Kibble EA, McCluskey NR, Mikucki EC, Thai VC, Stubbs KA, Sarkar-Tyson M, Kahler CM. Anti-Virulence Therapeutic Approaches for Neisseria gonorrhoeae. Antibiotics (Basel) 2021; 10:antibiotics10020103. [PMID: 33494538 PMCID: PMC7911339 DOI: 10.3390/antibiotics10020103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 01/15/2023] Open
Abstract
While antimicrobial resistance (AMR) is seen in both Neisseria gonorrhoeae and Neisseria meningitidis, the former has become resistant to commonly available over-the-counter antibiotic treatments. It is imperative then to develop new therapies that combat current AMR isolates whilst also circumventing the pathways leading to the development of AMR. This review highlights the growing research interest in developing anti-virulence therapies (AVTs) which are directed towards inhibiting virulence factors to prevent infection. By targeting virulence factors that are not essential for gonococcal survival, it is hypothesized that this will impart a smaller selective pressure for the emergence of resistance in the pathogen and in the microbiome, thus avoiding AMR development to the anti-infective. This review summates the current basis of numerous anti-virulence strategies being explored for N. gonorrhoeae.
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Affiliation(s)
- Katherine Y. L. Lim
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Christopher A. Mullally
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Ethan C. Haese
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Emily A. Kibble
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Nicolie R. McCluskey
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Edward C. Mikucki
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Van C. Thai
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Keith A. Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia;
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Charlene M. Kahler
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
- Correspondence:
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11
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A high-throughput cell-based assay pipeline for the preclinical development of bacterial DsbA inhibitors as antivirulence therapeutics. Sci Rep 2021; 11:1569. [PMID: 33452354 PMCID: PMC7810732 DOI: 10.1038/s41598-021-81007-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/17/2020] [Indexed: 11/23/2022] Open
Abstract
Antibiotics are failing fast, and the development pipeline remains alarmingly dry. New drug research and development is being urged by world health officials, with new antibacterials against multidrug-resistant Gram-negative pathogens as the highest priority. Antivirulence drugs, which inhibit bacterial pathogenicity factors, are a class of promising antibacterials, however, their development is stifled by lack of standardised preclinical testing akin to what guides antibiotic development. The lack of established target-specific microbiological assays amenable to high-throughput, often means that cell-based testing of virulence inhibitors is absent from the discovery (hit-to-lead) phase, only to be employed at later-stages of lead optimization. Here, we address this by establishing a pipeline of bacterial cell-based assays developed for the identification and early preclinical evaluation of DsbA inhibitors, previously identified by biophysical and biochemical assays. Inhibitors of DsbA block oxidative protein folding required for virulence factor folding in pathogens. Here we use existing Escherichia coli DsbA inhibitors and uropathogenic E. coli (UPEC) as a model pathogen, to demonstrate that the combination of a cell-based sulfotransferase assay and a motility assay (both DsbA reporter assays), modified for a higher throughput format, can provide a robust and target-specific platform for the identification and evaluation of DsbA inhibitors.
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Nebl S, Alwan WS, Williams ML, Sharma G, Taylor A, Doak BC, Wilde KL, McMahon RM, Halili MA, Martin JL, Capuano B, Fenwick RB, Mohanty B, Scanlon MJ. NMR fragment screening reveals a novel small molecule binding site near the catalytic surface of the disulfide-dithiol oxidoreductase enzyme DsbA from Burkholderia pseudomallei. JOURNAL OF BIOMOLECULAR NMR 2020; 74:595-611. [PMID: 32761504 DOI: 10.1007/s10858-020-00339-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
The presence of suitable cavities or pockets on protein structures is a general criterion for a therapeutic target protein to be classified as 'druggable'. Many disease-related proteins that function solely through protein-protein interactions lack such pockets, making development of inhibitors by traditional small-molecule structure-based design methods much more challenging. The 22 kDa bacterial thiol oxidoreductase enzyme, DsbA, from the gram-negative bacterium Burkholderia pseudomallei (BpsDsbA) is an example of one such target. The crystal structure of oxidized BpsDsbA lacks well-defined surface pockets. BpsDsbA is required for the correct folding of numerous virulence factors in B. pseudomallei, and genetic deletion of dsbA significantly attenuates B. pseudomallei virulence in murine infection models. Therefore, BpsDsbA is potentially an attractive drug target. Herein we report the identification of a small molecule binding site adjacent to the catalytic site of oxidized BpsDsbA. 1HN CPMG relaxation dispersion NMR measurements suggest that the binding site is formed transiently through protein dynamics. Using fragment-based screening, we identified a small molecule that binds at this site with an estimated affinity of KD ~ 500 µM. This fragment inhibits BpsDsbA enzymatic activity in vitro. The binding mode of this molecule has been characterized by NMR data-driven docking using HADDOCK. These data provide a starting point towards the design of more potent small molecule inhibitors of BpsDsbA.
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Affiliation(s)
- Stefan Nebl
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Wesam S Alwan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Martin L Williams
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Gaurav Sharma
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Ashley Taylor
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Bradley C Doak
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Karyn L Wilde
- National Deuteration Facility, Australian Nuclear Science and Technology Organization (ANSTO), Locked Bag 2001, Kirrawee DC, NSW, 2232, Australia
| | - Róisín M McMahon
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Maria A Halili
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Jennifer L Martin
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
- Vice-Chancellor's Unit, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Ben Capuano
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - R Bryn Fenwick
- Department of Integrative Structural and Computational Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
- ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
- ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
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Pandeya A, Ojo I, Alegun O, Wei Y. Periplasmic Targets for the Development of Effective Antimicrobials against Gram-Negative Bacteria. ACS Infect Dis 2020; 6:2337-2354. [PMID: 32786281 PMCID: PMC8187054 DOI: 10.1021/acsinfecdis.0c00384] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibiotic resistance has emerged as a serious threat to global public health in recent years. Lack of novel antimicrobials, especially new classes of compounds, further aggravates the situation. For Gram-negative bacteria, their double layered cell envelope and an array of efflux pumps act as formidable barriers for antimicrobials to penetrate. While cytoplasmic targets are hard to reach, proteins in the periplasm are clearly more accessible, as the drug only needs to breach the outer membrane. In this review, we summarized recent efforts on the validation and testing of periplasmic proteins as potential antimicrobial targets and the development of related inhibitors that either inhibit the growth of a bacterial pathogen or reduce its virulence during interaction with host cells. We conclude that the periplasm contains a promising pool of novel antimicrobial targets that should be scrutinized more closely for the development of effective treatment against multidrug-resistant Gram-negative bacteria.
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Affiliation(s)
- Ankit Pandeya
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Isoiza Ojo
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Olaniyi Alegun
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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14
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Li Q. Application of Fragment-Based Drug Discovery to Versatile Targets. Front Mol Biosci 2020; 7:180. [PMID: 32850968 PMCID: PMC7419598 DOI: 10.3389/fmolb.2020.00180] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is a powerful method to develop potent small-molecule compounds starting from fragments binding weakly to targets. As FBDD exhibits several advantages over high-throughput screening campaigns, it becomes an attractive strategy in target-based drug discovery. Many potent compounds/inhibitors of diverse targets have been developed using this approach. Methods used in fragment screening and understanding fragment-binding modes are critical in FBDD. This review elucidates fragment libraries, methods utilized in fragment identification/confirmation, strategies applied in growing the identified fragments into drug-like lead compounds, and applications of FBDD to different targets. As FBDD can be readily carried out through different biophysical and computer-based methods, it will play more important roles in drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangdong Academy of Sciences, Guangzhou, China
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Qian LL, Yi R, Min XT, Hu YC, Wan B, Chen QA. Rapid assembly of 3-azidomethylfurans from 2-(1-alkynyl)-2-alken-1-ones enabled by silver catalysis. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Diem Ferreira Xavier MC, Andia Sandagorda EM, Santos Neto JS, Schumacher RF, Silva MS. Synthesis of 3-selanylbenzo[ b]furans promoted by SelectFluor®. RSC Adv 2020; 10:13975-13983. [PMID: 35498450 PMCID: PMC9051628 DOI: 10.1039/d0ra01907k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 03/30/2020] [Indexed: 11/21/2022] Open
Abstract
A simple and practical protocol for the synthesis of 3-selanyl-benzo[b]furans mediated by the SelectFluor® reagent was developed. This novel methodology provided a greener alternative to generate 3-substituted-benzo[b]furans via a metal-free procedure under mild conditions. The intramolecular cyclization reaction was carried out employing an electrophilic selenium species generated in situ through the reaction between SelectFluor® and organic diselenides. The formation of this electrophilic selenium species (RSe-F) was confirmed by heteronuclear NMR spectroscopy, and its reactivity was explored.
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Affiliation(s)
- Maurício Carpe Diem Ferreira Xavier
- Laboratório de Síntese Orgânica Limpa - LASOL, Centro de Ciências Químicas, Farmacêuticas e de Alimentos - CCQFA, Universidade Federal de Pelotas - UFPel Capão do Leão RS Brazil
| | - Eduardo Martarelo Andia Sandagorda
- Laboratório de Síntese Orgânica Limpa - LASOL, Centro de Ciências Químicas, Farmacêuticas e de Alimentos - CCQFA, Universidade Federal de Pelotas - UFPel Capão do Leão RS Brazil
| | | | - Ricardo Frederico Schumacher
- Laboratório de Síntese Orgânica Limpa - LASOL, Centro de Ciências Químicas, Farmacêuticas e de Alimentos - CCQFA, Universidade Federal de Pelotas - UFPel Capão do Leão RS Brazil
- Departamento de Química, Universidade Federal de Santa Maria - UFSM Santa Maria RS Brazil
| | - Márcio Santos Silva
- Laboratório de Síntese Orgânica Limpa - LASOL, Centro de Ciências Químicas, Farmacêuticas e de Alimentos - CCQFA, Universidade Federal de Pelotas - UFPel Capão do Leão RS Brazil
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