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Li GC, Castro MA, Ukwaththage T, Sanders CR. Optimizing NMR fragment-based drug screening for membrane protein targets. J Struct Biol X 2024; 9:100100. [PMID: 38883400 PMCID: PMC11176934 DOI: 10.1016/j.yjsbx.2024.100100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/05/2024] [Accepted: 05/20/2024] [Indexed: 06/18/2024] Open
Abstract
NMR spectroscopy has played a pivotal role in fragment-based drug discovery by coupling detection of weak ligand-target binding with structural mapping of the binding site. Fragment-based screening by NMR has been successfully applied to many soluble protein targets, but only to a limited number of membrane proteins, despite the fact that many drug targets are membrane proteins. This is partly because of difficulties preparing membrane proteins for NMR-especially human membrane proteins-and because of the inherent complexity associated with solution NMR spectroscopy on membrane protein samples, which require the inclusion of membrane-mimetic agents such as micelles, nanodiscs, or bicelles. Here, we developed a generalizable protocol for fragment-based screening of membrane proteins using NMR. We employed two human membrane protein targets, both in fully protonated detergent micelles: the single-pass C-terminal domain of the amyloid precursor protein, C99, and the tetraspan peripheral myelin protein 22 (PMP22). For both we determined the optimal NMR acquisition parameters, protein concentration, protein-to-micelle ratio, and upper limit to the concentration of D6-DMSO in screening samples. Furthermore, we conducted preliminary screens of a plate-format molecular fragment mixture library using our optimized conditions and were able to identify hit compounds that selectively bound to the respective target proteins. It is hoped that the approaches presented here will be useful in complementing existing methods for discovering lead compounds that target membrane proteins.
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Affiliation(s)
- Geoffrey C Li
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine - Basic Sciences, Nashville, TN 37240, USA
| | - Manuel A Castro
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine - Basic Sciences, Nashville, TN 37240, USA
| | - Thilini Ukwaththage
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine - Basic Sciences, Nashville, TN 37240, USA
| | - Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine - Basic Sciences, Nashville, TN 37240, USA
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2
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Alghamdi MA, Azam F, Alam P. Deciphering Campylobacter jejuni DsbA1 protein dynamics in the presence of anti-virulent compounds: a multi-pronged computer-aided approach. J Biomol Struct Dyn 2024:1-17. [PMID: 38230450 DOI: 10.1080/07391102.2024.2302945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024]
Abstract
The current study aims to evaluate Asinex library compounds against Campylobacter jejuni DsbA1 protein, a thiol disulfide oxidoreductase enzyme that plays a major role in the oxidative folding of bacterial virulence proteins, making it a promising anti-viral drug target. By employing several techniques of computer-aided drug design, BDC25697459, BDD33601083, and BDC30129064 were identified with binding energy scores of -8.8 kcal/mol, -8.8 kcal/mol, and -8.3 kcal/mol, respectively. However, the control molecule, tetraethylene glycol, exhibited a binding energy score of -7.0 kcal/mol. The control, BDD33601083, and BDC30129064 were unveiled to bind the same co-crystallized binding site (pocket 1), while BDC25697459 interacted with a new binding pocket (pocket 2) adjacent to the control binding region. The molecular dynamics simulation showed that complexes exhibit stable dynamics without significant global or residue-level fluctuations. The average RMSD values were in the range of 2.07 Å-2.45 Å. Similarly, mean RMSF was recorded between 1.30 and 1.42 Å. The C. jejuni DsbA1 was also observed as compact in the presence of the compounds, showing a mean RoG value in the range of 16.42 Å-16.55 Å. In terms of MM/PBSA binding energy, the BDC30129064 complex was ranked top with -44.88 ± 4.14 kcal/mol, whereas the positive control molecule exhibited -22.22 ± 3.33 kcal/mol. From a pharmacokinetic perspective, the compounds are suitable candidates for clinical trial investigation. Preliminary computational analysis of these virtual hits indicates that these compounds have a low potential for ADME and toxicity-associated liabilities. In summary, the compounds displayed a high affinity for the C. jejuni DsbA1 protein, indicating potential efficacy that requires further investigation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mashael A Alghamdi
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
| | - Prawez Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia
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3
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Odenkirk MT, Zhang G, Marty MT. Do Nanodisc Assembly Conditions Affect Natural Lipid Uptake? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2006-2015. [PMID: 37524089 PMCID: PMC10528108 DOI: 10.1021/jasms.3c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Lipids play critical roles in modulating membrane protein structure, interactions, and activity. Nanodiscs provide a tunable membrane mimetic that can model these endogenous protein-lipid interactions in a nanoscale lipid bilayer. However, most studies of membrane proteins with nanodiscs use simple synthetic lipids that lack the headgroup and fatty acyl diversity of natural extracts. Prior research has successfully used natural lipid extracts in nanodiscs that more accurately mimic natural environments, but it is not clear how nanodisc assembly may bias the incorporated lipid profiles. Here, we applied lipidomics to investigate how nanodisc assembly conditions affect the profile of natural lipids in nanodiscs. Specifically, we tested the effects of assembly temperature, nanodisc size, and lipidome extract complexity. Globally, our analysis demonstrates that the lipids profiles are largely unaffected by nanodisc assembly conditions. However, a few notable changes emerged within individual lipids and lipid classes, such as a differential incorporation of cardiolipin and phosphatidylglycerol lipids from the E. coli polar lipid extract at different temperatures. Conversely, some classes of brain lipids were affected by nanodisc size at higher temperatures. Collectively, these data enable the application of nanodiscs to study protein-lipid interactions in complex lipid environments.
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Affiliation(s)
- Melanie T. Odenkirk
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ
- Bio5 Institute, University of Arizona, Tucson, AZ
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ
- Bio5 Institute, University of Arizona, Tucson, AZ
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4
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Zhao Z, Khurana A, Antony F, Young JW, Hewton KG, Brough Z, Zhong T, Parker SJ, Duong van Hoa F. A Peptidisc-Based Survey of the Plasma Membrane Proteome of a Mammalian Cell. Mol Cell Proteomics 2023; 22:100588. [PMID: 37295717 PMCID: PMC10416069 DOI: 10.1016/j.mcpro.2023.100588] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 05/05/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
Membrane proteins play critical roles at the cell surface and their misfunction is a hallmark of many human diseases. A precise evaluation of the plasma membrane proteome is therefore essential for cell biology and for discovering novel biomarkers and therapeutic targets. However, the low abundance of this proteome relative to soluble proteins makes it difficult to characterize, even with the most advanced proteomics technologies. Here, we apply the peptidisc membrane mimetic to purify the cell membrane proteome. Using the HeLa cell line as a reference, we capture 500 different integral membrane proteins, with half annotated to the plasma membrane. Notably, the peptidisc library is enriched with several ABC, SLC, GPCR, CD, and cell adhesion molecules that generally exist at low to very low copy numbers in the cell. We extend the method to compare two pancreatic cell lines, Panc-1 and hPSC. Here we observe a striking difference in the relative abundance of the cell surface cancer markers L1CAM, ANPEP, ITGB4, and CD70. We also identify two novel SLC transporters, SLC30A1 and SLC12A7, that are highly present in the Panc-1 cell only. The peptidisc library thus emerges as an effective way to survey and compare the membrane proteome of mammalian cells. Furthermore, since the method stabilizes membrane proteins in a water-soluble state, members of the library, here SLC12A7, can be specifically isolated.
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Affiliation(s)
- Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arshdeep Khurana
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Frank Antony
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - John W Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Keeley G Hewton
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Zora Brough
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tianshuang Zhong
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Seth J Parker
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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5
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Kerber PJ, Nuñez R, Jensen DR, Zhou AL, Peterson FC, Hill RB, Volkman BF, Smith BC. Fragment-based screening by protein-detected NMR spectroscopy. Methods Enzymol 2023; 690:285-310. [PMID: 37858532 PMCID: PMC10657026 DOI: 10.1016/bs.mie.2023.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Fragment-based drug discovery (FBDD) identifies low molecular weight compounds that can be developed into ligands with high affinity and selectivity for therapeutic targets. Screening fragment libraries (<10,000 molecules) with biophysical techniques against macromolecules provides information about novel chemical spaces that bind the macromolecule and scaffolds that can be modified to increase potency. A fragment-screening pipeline requires a standardized protocol for target selection, library assembly and maintenance, library screening, and hit validation to ensure hit integrity. Herein, the fundamental aspects of a fragment screening pipeline-focusing on protein-detected NMR data collection and analysis-are discussed in detail for researchers to use as a resource in their FBDD projects. Selected screening targets must undergo rigorous stability and buffer testing by NMR spectroscopy to ensure the protein structure is stable for the entire screen. Biophysical instrumentation that rapidly measures protein thermostability is helpful in buffer screening. Molecules in fragment libraries are analyzed computationally and physically, stored at appropriate temperatures, and multiplexed in well plates for library conservation. The screening protocol is streamlined using liquid handling robotics for sample preparation and customized Python scripts for protein-detected NMR data analysis. Molecules identified from the screen are titrated to determine their binding site(s) and Kd values and confirmed with an orthogonal biophysical assay. This detailed FBDD screening pipeline developed by the Program in Chemical Biology at the Medical College of Wisconsin has successfully screened many unrelated target proteins to identified novel molecules that selectively bind to these target proteins.
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Affiliation(s)
- Paul J Kerber
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Raymundo Nuñez
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Davin R Jensen
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Angela L Zhou
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States.
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States; Program in Chemical Biology, Medical College of Wisconsin, Watertown Plank Road, Milwaukee, WI, United States.
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6
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Kadeřábková N, Mahmood AJS, Furniss RCD, Mavridou DAI. Making a chink in their armor: Current and next-generation antimicrobial strategies against the bacterial cell envelope. Adv Microb Physiol 2023; 83:221-307. [PMID: 37507160 PMCID: PMC10517717 DOI: 10.1016/bs.ampbs.2023.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Gram-negative bacteria are uniquely equipped to defeat antibiotics. Their outermost layer, the cell envelope, is a natural permeability barrier that contains an array of resistance proteins capable of neutralizing most existing antimicrobials. As a result, its presence creates a major obstacle for the treatment of resistant infections and for the development of new antibiotics. Despite this seemingly impenetrable armor, in-depth understanding of the cell envelope, including structural, functional and systems biology insights, has promoted efforts to target it that can ultimately lead to the generation of new antibacterial therapies. In this article, we broadly overview the biology of the cell envelope and highlight attempts and successes in generating inhibitors that impair its function or biogenesis. We argue that the very structure that has hampered antibiotic discovery for decades has untapped potential for the design of novel next-generation therapeutics against bacterial pathogens.
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Affiliation(s)
- Nikol Kadeřábková
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Ayesha J S Mahmood
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - R Christopher D Furniss
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Despoina A I Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States; John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, TX, United States.
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7
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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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8
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Szigetvári Á, Szántay C. On the utility of nonuniformly sampled two-dimensional NMR spectra in the pharmaceutical industry. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:264-286. [PMID: 32754953 DOI: 10.1002/mrc.5085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/14/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
In this work, we discuss representative examples of the application of nonuniform sampling (NUS) in small-molecule structure determination in a pharmaceutical research and development and quality control setting. We demonstrate the advantages of NUS over traditional sampling in various industrial applications of nuclear magnetic resonance (NMR). We propose an optimal trade-off between the quality and the time efficiency of 'routine' measurements, as demonstrated via a test sample of vinpocetine analyzed on a 'work horse' NMR spectrometer. In addition, we present case studies where the application of NUS contributed significantly to the successful completion of some challenging structure determination task at hand. To that end, in some cases, we combined NUS with a method of decoupling in the indirect dimension that gives 'constant time' nuclear Overhauser effect spectroscopy (NOESY) and 'constant time' heteronuclear multiple bond correlation (HMBC) spectra. NUS proved to be superior over traditional sampling even for the analysis of trace impurities, where the need to cope with a thousand-fold or even larger dynamic range and low signal-to-noise ratio for the impurity signals is quite a challenge.
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Affiliation(s)
- Áron Szigetvári
- Spectroscopic Research Department, Gedeon Richter Plc., Budapest, Hungary
| | - Csaba Szántay
- Spectroscopic Research Department, Gedeon Richter Plc., Budapest, Hungary
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9
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Dhouib R, Vagenas D, Hong Y, Verderosa AD, Martin JL, Heras B, Totsika M. Antivirulence DsbA inhibitors attenuate Salmonella enterica serovar Typhimurium fitness without detectable resistance. FASEB Bioadv 2021; 3:231-242. [PMID: 33842848 PMCID: PMC8019255 DOI: 10.1096/fba.2020-00100] [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: 10/11/2020] [Revised: 12/22/2020] [Accepted: 01/06/2021] [Indexed: 11/15/2022] Open
Abstract
Inhibition of the DiSulfide Bond (DSB) oxidative protein folding machinery, a major facilitator of virulence in Gram‐negative bacteria, represents a promising antivirulence strategy. We previously developed small molecule inhibitors of DsbA from Escherichia coli K‐12 (EcDsbA) and showed that they attenuate virulence of Gram‐negative pathogens by directly inhibiting multiple diverse DsbA homologues. Here we tested the evolutionary robustness of DsbA inhibitors as antivirulence antimicrobials against Salmonella enterica serovar Typhimurium under pathophysiological conditions in vitro. We show that phenylthiophene DsbA inhibitors slow S. Typhimurium growth in minimal media, phenocopying S. Typhimurium isogenic dsbA null mutants. Through passaging experiments, we found that DsbA inhibitor resistance was not induced under conditions that rapidly induced resistance to ciprofloxacin, an antibiotic commonly used to treat Salmonella infections. Furthermore, no mutations were identified in the dsbA gene of inhibitor‐treated S. Typhimurium, and S. Typhimurium virulence remained susceptible to DsbA inhibitors. Our work demonstrates that under in vitro pathophysiological conditions, DsbA inhibitors can have both antivirulence and antibiotic action. Importantly, our finding that DsbA inhibitors appear to be evolutionarily robust offers promise for their further development as next‐generation antimicrobials against Gram‐negative pathogens.
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Affiliation(s)
- Rabeb Dhouib
- Institute of Health and Biomedical Innovation School of Biomedical Sciences Queensland University of Technology Herston QLD Australia.,Centre for Immunology and Infection Control School of Biomedical Sciences Queensland University of Technology Herston QLD Australia
| | - Dimitrios Vagenas
- Institute of Health and Biomedical Innovation School of Biomedical Sciences Queensland University of Technology Herston QLD Australia
| | - Yaoqin Hong
- Institute of Health and Biomedical Innovation School of Biomedical Sciences Queensland University of Technology Herston QLD Australia.,Centre for Immunology and Infection Control School of Biomedical Sciences Queensland University of Technology Herston QLD Australia
| | - Anthony D Verderosa
- Institute of Health and Biomedical Innovation School of Biomedical Sciences Queensland University of Technology Herston QLD Australia.,Centre for Immunology and Infection Control School of Biomedical Sciences Queensland University of Technology Herston QLD Australia
| | - Jennifer L Martin
- Griffith Institute for Drug Discovery Griffith University Nathan QLD Australia.,University of Wollongong Wollongong NSW Australia
| | - Begoña Heras
- La Trobe Institute for Molecular Science La Trobe University Bundoora VIC Australia
| | - Makrina Totsika
- Institute of Health and Biomedical Innovation School of Biomedical Sciences Queensland University of Technology Herston QLD Australia.,Centre for Immunology and Infection Control School of Biomedical Sciences Queensland University of Technology Herston QLD Australia
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10
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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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12
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Sligar SG, Denisov IG. Nanodiscs: A toolkit for membrane protein science. Protein Sci 2020; 30:297-315. [PMID: 33165998 DOI: 10.1002/pro.3994] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022]
Abstract
Membrane proteins are involved in numerous vital biological processes, including transport, signal transduction and the enzymes in a variety of metabolic pathways. Integral membrane proteins account for up to 30% of the human proteome and they make up more than half of all currently marketed therapeutic targets. Unfortunately, membrane proteins are inherently recalcitrant to study using the normal toolkit available to scientists, and one is most often left with the challenge of finding inhibitors, activators and specific antibodies using a denatured or detergent solubilized aggregate. The Nanodisc platform circumvents these challenges by providing a self-assembled system that renders typically insoluble, yet biologically and pharmacologically significant, targets such as receptors, transporters, enzymes, and viral antigens soluble in aqueous media in a native-like bilayer environment that maintain a target's functional activity. By providing a bilayer surface of defined composition and structure, Nanodiscs have found great utility in the study of cellular signaling complexes that assemble on a membrane surface. Nanodiscs provide a nanometer scale vehicle for the in vivo delivery of amphipathic drugs, therapeutic lipids, tethered nucleic acids, imaging agents and active protein complexes. This means for generating nanoscale lipid bilayers has spawned the successful use of numerous other polymer and peptide amphipathic systems. This review, in celebration of the Anfinsen Award, summarizes some recent results and provides an inroad into the current and historical literature.
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Affiliation(s)
- Stephen G Sligar
- Departments of Biochemistry Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Ilia G Denisov
- Departments of Biochemistry Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
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13
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Bushweller JH. Protein Disulfide Exchange by the Intramembrane Enzymes DsbB, DsbD, and CcdA. J Mol Biol 2020; 432:5091-5103. [PMID: 32305461 DOI: 10.1016/j.jmb.2020.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/06/2020] [Accepted: 04/08/2020] [Indexed: 12/29/2022]
Abstract
The formation of disulfide bonds in proteins is an essential process in both prokaryotes and eukaryotes. In gram-negative bacteria including Escherichia coli, the proteins DsbA and DsbB mediate the formation of disulfide bonds in the periplasm. DsbA acts as the periplasmic oxidant of periplasmic substrate proteins. DsbA is reoxidized by transfer of reducing equivalents to the 4 TM helix membrane protein DsbB, which transfers reducing equivalents to ubiquinone or menaquinone. Multiple structural studies of DsbB have provided detailed structural information on intermediates in the process of DsbB catalyzed oxidation of DsbA. These structures and the insights gained are described. In proteins with more than one pair of Cys residues, there is the potential for formation of non-native disulfide bonds, making it necessary for the cell to have a mechanism for the isomerization of such non-native disulfide bonds. In E. coli, this is mediated by the proteins DsbC and DsbD. DsbC reduces mis-formed disulfide bonds. The eight-TM-helix protein DsbD reduces DsbC and is itself reduced by cytoplasmic thioredoxin. DsbD also contributes reducing equivalents for the reduction of cytochrome c to facilitate heme attachment. The DsbD functional homolog CcdA is a six-TM-helix membrane protein that provides reducing equivalents for the reduction of cytochrome c. A recent structure determination of CcdA has provided critical insights into how reducing equivalents are transferred across the membrane that likely also provides understanding how this is achieved by DsbD as well. This structure and the insights gained are described.
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Affiliation(s)
- John H Bushweller
- Department of Molecular Physiology and Biological Physics, Department of Chemistry, University of Virginia, Charlottesville, VA 22903, USA.
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14
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The Fragment-Based Development of a Benzofuran Hit as a New Class of Escherichia coli DsbA Inhibitors. Molecules 2019; 24:molecules24203756. [PMID: 31635355 PMCID: PMC6832960 DOI: 10.3390/molecules24203756] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/13/2019] [Accepted: 10/15/2019] [Indexed: 11/17/2022] Open
Abstract
A fragment-based drug discovery approach was taken to target the thiol-disulfide oxidoreductase enzyme DsbA from Escherichia coli (EcDsbA). This enzyme is critical for the correct folding of virulence factors in many pathogenic Gram-negative bacteria, and small molecule inhibitors can potentially be developed as anti-virulence compounds. Biophysical screening of a library of fragments identified several classes of fragments with affinity to EcDsbA. One hit with high mM affinity, 2-(6-bromobenzofuran-3-yl)acetic acid (6), was chemically elaborated at several positions around the scaffold. X-ray crystal structures of the elaborated analogues showed binding in the hydrophobic binding groove adjacent to the catalytic disulfide bond of EcDsbA. Binding affinity was calculated based on NMR studies and compounds 25 and 28 were identified as the highest affinity binders with dissociation constants (KD) of 326 ± 25 and 341 ± 57 µM respectively. This work suggests the potential to develop benzofuran fragments into a novel class of EcDsbA inhibitors.
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15
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Banaś AM, Bocian-Ostrzycka KM, Jagusztyn-Krynicka EK. Engineering of the Dsb (disulfide bond) proteins - contribution towards understanding their mechanism of action and their applications in biotechnology and medicine. Crit Rev Microbiol 2019; 45:433-450. [PMID: 31190593 DOI: 10.1080/1040841x.2019.1622509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Dsb protein family in prokaryotes catalyzes the generation of disulfide bonds between thiol groups of cysteine residues in nascent proteins, ensuring their proper three-dimensional structure; these bonds are crucial for protein stability and function. The first Dsb protein, Escherichia coli DsbA, was described in 1991. Since then, many details of the bond-formation process have been described through microbiological, biochemical, biophysical and bioinformatics strategies. Research with the model microorganism E. coli and many other bacterial species revealed an enormous diversity of bond-formation mechanisms. Research using Dsb protein engineering has significantly helped to reveal details of the disulfide bond formation. The first part of this review presents the research that led to understanding the mechanism of action of DsbA proteins, which directly transfer their own disulfide into target proteins. The second part concentrates on the mechanism of electron transport through the cell cytoplasmic membrane. Third and lastly, the review discusses the contribution of this research towards new antibacterial agents.
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Affiliation(s)
- Anna Marta Banaś
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw , Miecznikowa 1 , Warsaw , Poland
| | - Katarzyna Marta Bocian-Ostrzycka
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw , Miecznikowa 1 , Warsaw , Poland
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16
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Christensen S, McMahon RM, Martin JL, Huston WM. Life inside and out: making and breaking protein disulfide bonds in Chlamydia. Crit Rev Microbiol 2019; 45:33-50. [PMID: 30663449 DOI: 10.1080/1040841x.2018.1538933] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Disulphide bonds are widely used among all domains of life to provide structural stability to proteins and to regulate enzyme activity. Chlamydia spp. are obligate intracellular bacteria that are especially dependent on the formation and degradation of protein disulphide bonds. Members of the genus Chlamydia have a unique biphasic developmental cycle alternating between two distinct cell types; the extracellular infectious elementary body (EB) and the intracellular replicating reticulate body. The proteins in the envelope of the EB are heavily cross-linked with disulphides and this is known to be critical for this infectious phase. In this review, we provide a comprehensive summary of what is known about the redox state of chlamydial envelope proteins throughout the developmental cycle. We focus especially on the factors responsible for degradation and formation of disulphide bonds in Chlamydia and how this system compares with redox regulation in other organisms. Focussing on the unique biology of Chlamydia enables us to provide important insights into how specialized suites of disulphide bond (Dsb) proteins cater for specific bacterial environments and lifecycles.
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Affiliation(s)
- Signe Christensen
- a Division of Chemistry and Structural Biology , Institute for Molecular Bioscience, University of Queensland , St. Lucia , QLD , Australia.,b Griffith Institute for Drug Discovery, Griffith University , Nathan , QLD , Australia
| | - Róisín M McMahon
- b Griffith Institute for Drug Discovery, Griffith University , Nathan , QLD , Australia
| | - Jennifer L Martin
- b Griffith Institute for Drug Discovery, Griffith University , Nathan , QLD , Australia
| | - Wilhelmina M Huston
- c School of Life Sciences , University of Technology Sydney , Ultimo , NSW , Australia
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17
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Heikal A, Nakatani Y, Jiao W, Wilson C, Rennison D, Weimar MR, Parker EJ, Brimble MA, Cook GM. 'Tethering' fragment-based drug discovery to identify inhibitors of the essential respiratory membrane protein type II NADH dehydrogenase. Bioorg Med Chem Lett 2018; 28:2239-2243. [PMID: 29859905 DOI: 10.1016/j.bmcl.2018.05.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/22/2018] [Accepted: 05/25/2018] [Indexed: 10/16/2022]
Abstract
Energy generation is a promising area of drug discovery for both bacterial pathogens and parasites. Type II NADH dehydrogenase (NDH-2), a vital respiratory membrane protein, has attracted attention as a target for the development of new antitubercular and antimalarial agents. To date, however, no potent, specific inhibitors have been identified. Here, we performed a site-directed screening technique, tethering-fragment based drug discovery, against wild-type and mutant forms of NDH-2 containing engineered active-site cysteines. Inhibitory fragments displayed IC50 values between 3 and 110 μM against NDH-2 mutants. Possible binding poses were investigated by in silico modelling, providing a basis for optimisation of fragment binding and improved potency against NDH-2.
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Affiliation(s)
- Adam Heikal
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Yoshio Nakatani
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Wanting Jiao
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Chris Wilson
- Small Molecule Discovery Center, University of California, San Francisco, San Francisco, CA 94143, United States
| | - David Rennison
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Marion R Weimar
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Margaret A Brimble
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
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18
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Virulence of the Melioidosis Pathogen Burkholderia pseudomallei Requires the Oxidoreductase Membrane Protein DsbB. Infect Immun 2018; 86:IAI.00938-17. [PMID: 29440370 PMCID: PMC5913862 DOI: 10.1128/iai.00938-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/04/2018] [Indexed: 12/26/2022] Open
Abstract
The naturally antibiotic-resistant bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a disease with stubbornly high mortality and a complex, protracted treatment regimen. The worldwide incidence of melioidosis is likely grossly underreported, though it is known to be highly endemic in northern Australia and Southeast Asia. Bacterial disulfide bond (DSB) proteins catalyze the oxidative folding and isomerization of disulfide bonds in substrate proteins. In the present study, we demonstrate that B. pseudomallei membrane protein disulfide bond protein B (BpsDsbB) forms a functional redox relay with the previously characterized virulence mediator B. pseudomallei disulfide bond protein A (BpsDsbA). Genomic analysis of diverse B. pseudomallei clinical isolates demonstrated that dsbB is a highly conserved core gene. Critically, we show that DsbB is required for virulence in B. pseudomallei. A panel of B. pseudomalleidsbB deletion strains (K96243, 576, MSHR2511, MSHR0305b, and MSHR5858) were phenotypically diverse according to the results of in vitro assays that assess hallmarks of virulence. Irrespective of their in vitro virulence phenotypes, two deletion strains were attenuated in a BALB/c mouse model of infection. A crystal structure of a DsbB-derived peptide complexed with BpsDsbA provides the first molecular characterization of their interaction. This work contributes to our broader understanding of DSB redox biology and will support the design of antimicrobial drugs active against this important family of bacterial virulence targets.
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19
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Landeta C, Boyd D, Beckwith J. Disulfide bond formation in prokaryotes. Nat Microbiol 2018; 3:270-280. [PMID: 29463925 DOI: 10.1038/s41564-017-0106-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 12/21/2017] [Indexed: 12/25/2022]
Abstract
Interest in protein disulfide bond formation has recently increased because of the prominent role of disulfide bonds in bacterial virulence and survival. The first discovered pathway that introduces disulfide bonds into cell envelope proteins consists of Escherichia coli enzymes DsbA and DsbB. Since its discovery, variations on the DsbAB pathway have been found in bacteria and archaea, probably reflecting specific requirements for survival in their ecological niches. One variation found amongst Actinobacteria and Cyanobacteria is the replacement of DsbB by a homologue of human vitamin K epoxide reductase. Many Gram-positive bacteria express enzymes involved in disulfide bond formation that are similar, but non-homologous, to DsbAB. While bacterial pathways promote disulfide bond formation in the bacterial cell envelope, some archaeal extremophiles express proteins with disulfide bonds both in the cytoplasm and in the extra-cytoplasmic space, possibly to stabilize proteins in the face of extreme conditions, such as growth at high temperatures. Here, we summarize the diversity of disulfide-bond-catalysing systems across prokaryotic lineages, discuss examples for understanding the biological basis of such systems, and present perspectives on how such systems are enabling advances in biomedical engineering and drug development.
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Affiliation(s)
- Cristina Landeta
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Dana Boyd
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Jon Beckwith
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
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20
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Cerofolini L, Giuntini S, Louka A, Ravera E, Fragai M, Luchinat C. High-Resolution Solid-State NMR Characterization of Ligand Binding to a Protein Immobilized in a Silica Matrix. J Phys Chem B 2017; 121:8094-8101. [PMID: 28762736 DOI: 10.1021/acs.jpcb.7b05679] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Solid-state NMR is becoming a powerful tool to detect atomic-level structural features of biomolecules even when they are bound to (or trapped in) solid systems that lack long-range three-dimensional order. We here demonstrate that it is possible to probe protein-ligand interactions from a protein-based perspective also when the protein is entrapped in silica, thus translating into biomolecular solid-state NMR all of the considerations that are usually made to understand the chemical nature of the interaction of a protein with its ligands. This work provides a proof of concept that also immobilized enzymes can be used for protein-based NMR protein-ligand interactions for drug discovery.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Alexandra Louka
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.,GiottoBiotech S.R.L. , Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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21
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Huber S, Casagrande F, Hug MN, Wang L, Heine P, Kummer L, Plückthun A, Hennig M. SPR-based fragment screening with neurotensin receptor 1 generates novel small molecule ligands. PLoS One 2017; 12:e0175842. [PMID: 28510609 PMCID: PMC5433701 DOI: 10.1371/journal.pone.0175842] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 04/01/2017] [Indexed: 12/22/2022] Open
Abstract
The neurotensin receptor 1 represents an important drug target involved in various diseases of the central nervous system. So far, the full exploitation of potential therapeutic activities has been compromised by the lack of compounds with favorable physicochemical and pharmacokinetic properties which efficiently penetrate the blood-brain barrier. Recent progress in the generation of stabilized variants of solubilized neurotensin receptor 1 and its subsequent purification and successful structure determination presents a solid starting point to apply the approach of fragment-based screening to extend the chemical space of known neurotensin receptor 1 ligands. In this report, surface plasmon resonance was used as primary method to screen 6369 compounds. Thereby 44 hits were identified and confirmed in competition as well as dose-response experiments. Furthermore, 4 out of 8 selected hits were validated using nuclear magnetic resonance spectroscopy as orthogonal biophysical method. Computational analysis of the compound structures, taking the known crystal structure of the endogenous peptide agonist into consideration, gave insight into the potential fragment-binding location and interactions and inspires chemistry efforts for further exploration of the fragments.
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Affiliation(s)
- Sylwia Huber
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
- * E-mail: (SH); (MH)
| | - Fabio Casagrande
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
| | - Melanie N. Hug
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
| | - Lisha Wang
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
| | - Philipp Heine
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Lutz Kummer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Michael Hennig
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
- * E-mail: (SH); (MH)
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22
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Bacterial thiol oxidoreductases - from basic research to new antibacterial strategies. Appl Microbiol Biotechnol 2017; 101:3977-3989. [PMID: 28409380 PMCID: PMC5403849 DOI: 10.1007/s00253-017-8291-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 12/15/2022]
Abstract
The recent, rapid increase in bacterial antimicrobial resistance has become a major public health concern. One approach to generate new classes of antibacterials is targeting virulence rather than the viability of bacteria. Proteins of the Dsb system, which play a key role in the virulence of many pathogenic microorganisms, represent potential new drug targets. The first part of the article presents current knowledge of how the Dsb system impacts function of various protein secretion systems that influence the virulence of many pathogenic bacteria. Next, the review describes methods used to study the structure, biochemistry, and microbiology of the Dsb proteins and shows how these experiments broaden our knowledge about their function. The lessons gained from basic research have led to a specific search for inhibitors blocking the Dsb networks.
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23
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Abstract
Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
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24
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Li Q, Qiao P, Chen X, Wang J, Bian L, Zheng X. Affinity chromatographic methodologies based on immobilized voltage dependent anion channel isoform 1 and application in protein-ligand interaction analysis and bioactive compounds screening from traditional medicine. J Chromatogr A 2017; 1495:31-45. [PMID: 28342583 DOI: 10.1016/j.chroma.2017.03.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/09/2017] [Accepted: 03/13/2017] [Indexed: 12/11/2022]
Abstract
Voltage dependent anion channel isoform 1 (VDAC-1) serves as an attractive target of anti-cancer drugs by mediating the entry and exit of metabolites between cytoplasm and mitochondria. This work reports on the preparation of a VDAC-1-based bioaffinity chromatographic stationary phase by linking the protein on lecithin modified microspheres. An assay of chromatographic methods including frontal analysis, zonal elution, injection dependent analysis and nonlinear chromatography were utilized to investigate the bindings of ATP, NADH and NADPH to VDAC-1. Electrostatic interactions were found to be main forces during these bindings. The calculated association constants of the three ligands to VDAC-1 showed good agreements between diverse chromatographic methods. Validated application of the stationary phase was performed by screening anti-cancer compounds of Rheum officinale Baill. using high performance affinity chromatography coupled with electrospray ionization-quadrupole time of flight mass spectrometry. Chrysophanol, emodin, rhein, aloe-emodin and catechin were identified as the bioactive components of the herb. These compounds targeted VDAC-1 through Thr207 and the N-terminal region of the protein. Taken together, the current stationary phase was possible to become a promising tool for protein-ligand interaction analysis and anti-cancer drug screening from complex matrices.
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Affiliation(s)
- Qian Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Pan Qiao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xiu Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jing Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Liujiao Bian
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Xiaohui Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
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25
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Renaud JP, Chung CW, Danielson UH, Egner U, Hennig M, Hubbard RE, Nar H. Biophysics in drug discovery: impact, challenges and opportunities. Nat Rev Drug Discov 2016; 15:679-98. [PMID: 27516170 DOI: 10.1038/nrd.2016.123] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past 25 years, biophysical technologies such as X-ray crystallography, nuclear magnetic resonance spectroscopy, surface plasmon resonance spectroscopy and isothermal titration calorimetry have become key components of drug discovery platforms in many pharmaceutical companies and academic laboratories. There have been great improvements in the speed, sensitivity and range of possible measurements, providing high-resolution mechanistic, kinetic, thermodynamic and structural information on compound-target interactions. This Review provides a framework to understand this evolution by describing the key biophysical methods, the information they can provide and the ways in which they can be applied at different stages of the drug discovery process. We also discuss the challenges for current technologies and future opportunities to use biophysical methods to solve drug discovery problems.
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Affiliation(s)
- Jean-Paul Renaud
- NovAliX, Boulevard Sébastien Brant, 67405 Illkirch Cedex, France.,Institut de Génétique et Biologie Moléculaire et Cellulaire, CNRS UMR7104/INSERM U964/Université de Strasbourg, 1 rue Laurent Fries - BP10142, 67404 Illkirch Cedex, France.,RiboStruct, 15 rue Neuve, 67540 Ostwald, France
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - U Helena Danielson
- Department of Chemistry - BMC and Science for Life Laboratory, Drug Discovery &Development Platform, Uppsala University, SE-751 05 Uppsala, Sweden.,Beactica AB, Uppsala Business Park, 754 50 Uppsala, Sweden
| | - Ursula Egner
- Bayer Pharma AG, Müllerstrasse 178, 13353 Berlin, Germany
| | - Michael Hennig
- Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland.,leadXpro AG, PARK INNOVAARE, CH-5234 Villigen, Switzerland
| | - Roderick E Hubbard
- University of York, Heslington, York, YO10 5DD, UK.,Vernalis (R&D), Granta Park, Cambridge, CB21 6GB, UK
| | - Herbert Nar
- Boehringer Ingelheim GmbH &Co. KG, Birkendorfer Strasse 65, 88400 Biberach, Germany
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26
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Smith RP, Paxman JJ, Scanlon MJ, Heras B. Targeting Bacterial Dsb Proteins for the Development of Anti-Virulence Agents. Molecules 2016; 21:molecules21070811. [PMID: 27438817 PMCID: PMC6273893 DOI: 10.3390/molecules21070811] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 05/21/2016] [Accepted: 05/25/2016] [Indexed: 11/22/2022] Open
Abstract
Recent years have witnessed a dramatic increase in bacterial antimicrobial resistance and a decline in the development of novel antibiotics. New therapeutic strategies are urgently needed to combat the growing threat posed by multidrug resistant bacterial infections. The Dsb disulfide bond forming pathways are potential targets for the development of antimicrobial agents because they play a central role in bacterial pathogenesis. In particular, the DsbA/DsbB system catalyses disulfide bond formation in a wide array of virulence factors, which are essential for many pathogens to establish infections and cause disease. These redox enzymes are well placed as antimicrobial targets because they are taxonomically widespread, share low sequence identity with human proteins, and many years of basic research have provided a deep molecular understanding of these systems in bacteria. In this review, we discuss disulfide bond catalytic pathways in bacteria and their significance in pathogenesis. We also review the use of different approaches to develop inhibitors against Dsb proteins as potential anti-virulence agents, including fragment-based drug discovery, high-throughput screening and other structure-based drug discovery methods.
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Affiliation(s)
- Roxanne P Smith
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, Vic 3083, Australia.
| | - Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, Vic 3083, Australia.
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Royal Parade, Parkville, Vic 3052, Australia.
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, Vic 3083, Australia.
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27
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Hao GF, Jiang W, Ye YN, Wu FX, Zhu XL, Guo FB, Yang GF. ACFIS: a web server for fragment-based drug discovery. Nucleic Acids Res 2016; 44:W550-6. [PMID: 27150808 PMCID: PMC4987934 DOI: 10.1093/nar/gkw393] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/28/2016] [Indexed: 11/14/2022] Open
Abstract
In order to foster innovation and improve the effectiveness of drug discovery, there is a considerable interest in exploring unknown ‘chemical space’ to identify new bioactive compounds with novel and diverse scaffolds. Hence, fragment-based drug discovery (FBDD) was developed rapidly due to its advanced expansive search for ‘chemical space’, which can lead to a higher hit rate and ligand efficiency (LE). However, computational screening of fragments is always hampered by the promiscuous binding model. In this study, we developed a new web server Auto Core Fragment in silico Screening (ACFIS). It includes three computational modules, PARA_GEN, CORE_GEN and CAND_GEN. ACFIS can generate core fragment structure from the active molecule using fragment deconstruction analysis and perform in silico screening by growing fragments to the junction of core fragment structure. An integrated energy calculation rapidly identifies which fragments fit the binding site of a protein. We constructed a simple interface to enable users to view top-ranking molecules in 2D and the binding mode in 3D for further experimental exploration. This makes the ACFIS a highly valuable tool for drug discovery. The ACFIS web server is free and open to all users at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS/.
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Affiliation(s)
- Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China
| | - Wen Jiang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China
| | - Yuan-Nong Ye
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjing 300072, P.R.China
| | - Feng-Xu Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China
| | - Feng-Biao Guo
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjing 300072, P.R.China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China Collaborative Innovation Center of Chemical Science and Engineering, Tianjing 300072, P.R.China
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28
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Guo D, Heitman LH, IJzerman AP. Kinetic Aspects of the Interaction between Ligand and G Protein-Coupled Receptor: The Case of the Adenosine Receptors. Chem Rev 2016; 117:38-66. [DOI: 10.1021/acs.chemrev.6b00025] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dong Guo
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Laura H. Heitman
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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29
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Fragment Screening of Human Aquaporin 1. Int J Mol Sci 2016; 17:449. [PMID: 27023529 PMCID: PMC4848905 DOI: 10.3390/ijms17040449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/14/2016] [Accepted: 03/18/2016] [Indexed: 11/17/2022] Open
Abstract
Aquaporins (AQPs) are membrane proteins that enable water transport across cellular plasma membranes in response to osmotic gradients. Phenotypic analyses have revealed important physiological roles for AQPs, and the potential for AQP water channel modulators in various disease states has been proposed. For example, AQP1 is overexpressed in tumor microvessels, and this correlates with higher metastatic potential and aggressiveness of the malignancy. Chemical modulators would help in identifying the precise contribution of water channel activity in these disease states. These inhibitors would also be important therapeutically, e.g., in anti-cancer treatment. This perceived importance contrasts with the lack of success of high-throughput screens (HTS) to identify effective and specific inhibitors of aquaporins. In this paper, we have screened a library of 1500 "fragments", i.e., smaller than molecules used in HTS, against human aquaporin (hAQP1) using a thermal shift assay and surface plasmon resonance. Although these fragments may not inhibit their protein target, they bound to and stabilized hAQP1 (sub mM binding affinities (KD), with an temperature of aggregation shift ΔTagg of +4 to +50 °C) in a concentration-dependent fashion. Chemically expanded versions of these fragments should follow the determination of their binding site on the aquaporin surface.
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30
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Heras B, Scanlon MJ, Martin JL. Targeting virulence not viability in the search for future antibacterials. Br J Clin Pharmacol 2015; 79:208-15. [PMID: 24552512 DOI: 10.1111/bcp.12356] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/09/2013] [Indexed: 01/01/2023] Open
Abstract
New antibacterials need new approaches to overcome the problem of rapid antibiotic resistance. Here we review the development of potential new antibacterial drugs that do not kill bacteria or inhibit their growth, but combat disease instead by targeting bacterial virulence.
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Affiliation(s)
- Begoña Heras
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Vic
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31
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Zhang R, Sahu ID, Gibson KR, Muhammad NB, Bali AP, Comer RG, Liu L, Craig AF, Mccarrick RM, Dabney-Smith C, Sanders CR, Lorigan GA. Development of electron spin echo envelope modulation spectroscopy to probe the secondary structure of recombinant membrane proteins in a lipid bilayer. Protein Sci 2015; 24:1707-13. [PMID: 26355804 DOI: 10.1002/pro.2795] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 12/19/2022]
Abstract
Membrane proteins conduct many important biological functions essential to the survival of organisms. However, due to their inherent hydrophobic nature, it is very difficult to obtain structural information on membrane-bound proteins using traditional biophysical techniques. We are developing a new approach to probe the secondary structure of membrane proteins using the pulsed EPR technique of Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. This method has been successfully applied to model peptides made synthetically. However, in order for this ESEEM technique to be widely applicable to larger membrane protein systems with no size limitations, protein samples with deuterated residues need to be prepared via protein expression methods. For the first time, this study shows that the ESEEM approach can be used to probe the local secondary structure of a (2) H-labeled d8 -Val overexpressed membrane protein in a membrane mimetic environment. The membrane-bound human KCNE1 protein was used with a known solution NMR structure to demonstrate the applicability of this methodology. Three different α-helical regions of KCNE1 were probed: the extracellular domain (Val21), transmembrane domain (Val50), and cytoplasmic domain (Val95). These results indicated α-helical structures in all three segments, consistent with the micelle structure of KCNE1. Furthermore, KCNE1 was incorporated into a lipid bilayer and the secondary structure of the transmembrane domain (Val50) was shown to be α-helical in a more native-like environment. This study extends the application of this ESEEM approach to much larger membrane protein systems that are difficult to study with X-ray crystallography and/or NMR spectroscopy.
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Affiliation(s)
- Rongfu Zhang
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Kaylee R Gibson
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Nefertiti B Muhammad
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Avnika P Bali
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Raven G Comer
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Lishan Liu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Robert M Mccarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Carole Dabney-Smith
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, 37232
| | - Gary A Lorigan
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
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32
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Biosensor-based affinities and binding kinetics of small molecule antagonists to the adenosine A(2A) receptor reconstituted in HDL like particles. FEBS Lett 2015; 589:1399-405. [PMID: 25935416 DOI: 10.1016/j.febslet.2015.04.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/14/2015] [Accepted: 04/17/2015] [Indexed: 11/23/2022]
Abstract
The options for investigating solubilised G protein-coupled receptors (GPCRs) by biophysical techniques have long been hampered by their instability. A thermostabilised adenosine A2A receptor expressed in insect cells, purified in detergent and reconstituted into high-density lipoprotein (HDL) particles was immobilised onto a Surface Plasmon Resonance sensor chip. This allowed measurement of affinities and kinetics for A2A antagonists with affinities ranging from 50 pM to almost 2 μM. Compared with other formats, reproduction of affinities, and dissociation and association rate constants are good, reasonable and poor respectively, indicating stabilised receptors in HDL particles are useful for investigating specific aspects of GPCR-ligand interactions.
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33
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Halili MA, Bachu P, Lindahl F, Bechara C, Mohanty B, Reid RC, Scanlon MJ, Robinson CV, Fairlie DP, Martin JL. Small molecule inhibitors of disulfide bond formation by the bacterial DsbA-DsbB dual enzyme system. ACS Chem Biol 2015; 10:957-64. [PMID: 25603425 DOI: 10.1021/cb500988r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The DsbA:DsbB redox machinery catalyzes disulfide bond formation in secreted proteins and is required for bacterial virulence factor assembly. Both enzymes have been identified as targets for antivirulence drugs. Here, we report synthetic analogues of ubiquinone (dimedone derivatives) that inhibit disulfide bond formation (IC50∼1 μM) catalyzed by E. coli DsbA:DsbB. The mechanism involves covalent modification of a single free cysteine leaving other cysteines unmodified. A vinylogous anhydride in each inhibitor is cleaved by the thiol, which becomes covalently modified to a thioester by a propionyl substituent. Cysteines and lysines on DsbA and DsbB and a nonredox enzyme were modified in a manner that implies some specificity. Moreover, human thioredoxin was not inhibited under the same conditions that inhibited EcDsbA. This proof of concept work uses small molecules that target specific cysteines to validate the DsbA and DsbB dual enzyme system as a viable and potentially druggable antivirulence target.
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Affiliation(s)
- Maria A. Halili
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Prabhakar Bachu
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Fredrik Lindahl
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Chérine Bechara
- Department
of Chemistry, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Biswaranjan Mohanty
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Robert C. Reid
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Martin J. Scanlon
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Carol V. Robinson
- Department
of Chemistry, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David P. Fairlie
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Jennifer L. Martin
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
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34
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Landeta C, Blazyk JL, Hatahet F, Meehan BM, Eser M, Myrick A, Bronstain L, Minami S, Arnold H, Ke N, Rubin EJ, Furie BC, Furie B, Beckwith J, Dutton R, Boyd D. Compounds targeting disulfide bond forming enzyme DsbB of Gram-negative bacteria. Nat Chem Biol 2015; 11:292-8. [PMID: 25686372 PMCID: PMC4366281 DOI: 10.1038/nchembio.1752] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 12/18/2014] [Indexed: 01/18/2023]
Abstract
In bacteria, disulfide bonds confer stability on many proteins exported to the cell envelope or beyond. These proteins include numerous bacterial virulence factors, and thus bacterial enzymes that promote disulfide bond formation represent targets for compounds inhibiting bacterial virulence. Here, we describe a new target- and cell-based screening methodology for identifying compounds that inhibit the disulfide bond-forming enzymes Escherichia coli DsbB (EcDsbB) or Mycobacterium tuberculosis VKOR (MtbVKOR), which can replace EcDsbB, although the two are not homologs. Initial screening of 51,487 compounds yielded six specifically inhibiting EcDsbB. These compounds share a structural motif and do not inhibit MtbVKOR. A medicinal chemistry approach led us to select related compounds, some of which are much more effective DsbB inhibitors than those found in the screen. These compounds inhibit purified DsbB and prevent anaerobic growth of E. coli. Furthermore, these compounds inhibit all but one of the DsbBs of nine other Gram-negative pathogenic bacteria tested.
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Affiliation(s)
- Cristina Landeta
- Department of Microbiology and Immunobiology. Harvard Medical School, Boston, MA 02115, USA
| | - Jessica L. Blazyk
- Department of Microbiology and Immunobiology. Harvard Medical School, Boston, MA 02115, USA
| | - Feras Hatahet
- Department of Microbiology and Immunobiology. Harvard Medical School, Boston, MA 02115, USA
| | - Brian M. Meehan
- Department of Microbiology and Immunobiology. Harvard Medical School, Boston, MA 02115, USA
| | - Markus Eser
- Department of Microbiology and Immunobiology. Harvard Medical School, Boston, MA 02115, USA
| | - Alissa Myrick
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Ludmila Bronstain
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Shoko Minami
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | | | | | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Barbara C. Furie
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Bruce Furie
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Jon Beckwith
- Department of Microbiology and Immunobiology. Harvard Medical School, Boston, MA 02115, USA
| | | | - Dana Boyd
- Department of Microbiology and Immunobiology. Harvard Medical School, Boston, MA 02115, USA
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35
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Quantitative and Systems-Based Approaches for Deciphering Bacterial Membrane Interactome and Gene Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:135-54. [PMID: 26621466 DOI: 10.1007/978-3-319-23603-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
High-throughput genomic and proteomic methods provide a concise description of the molecular constituents of a cell, whereas systems biology strives to understand the way these components function as a whole. Recent developments, such as genome editing technologies and protein epitope-tagging coupled with high-sensitivity mass-spectrometry, allow systemic studies to be performed at an unprecedented scale. Available methods can be successfully applied to various goals, both expanding fundamental knowledge and solving applied problems. In this review, we discuss the present state and future of bacterial cell envelope interactomics, with a specific focus on host-pathogen interactions and drug target discovery. Both experimental and computational methods will be outlined together with examples of their practical implementation.
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36
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Adams LA, Sharma P, Mohanty B, Ilyichova OV, Mulcair MD, Williams ML, Gleeson EC, Totsika M, Doak BC, Caria S, Rimmer K, Horne J, Shouldice SR, Vazirani M, Headey SJ, Plumb BR, Martin JL, Heras B, Simpson JS, Scanlon MJ. Application of Fragment-Based Screening to the Design of Inhibitors ofEscherichia coliDsbA. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Adams LA, Sharma P, Mohanty B, Ilyichova OV, Mulcair MD, Williams ML, Gleeson EC, Totsika M, Doak BC, Caria S, Rimmer K, Horne J, Shouldice SR, Vazirani M, Headey SJ, Plumb BR, Martin JL, Heras B, Simpson JS, Scanlon MJ. Application of fragment-based screening to the design of inhibitors of Escherichia coli DsbA. Angew Chem Int Ed Engl 2014; 54:2179-84. [PMID: 25556635 DOI: 10.1002/anie.201410341] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/25/2014] [Indexed: 12/11/2022]
Abstract
The thiol-disulfide oxidoreductase enzyme DsbA catalyzes the formation of disulfide bonds in the periplasm of Gram-negative bacteria. DsbA substrates include proteins involved in bacterial virulence. In the absence of DsbA, many of these proteins do not fold correctly, which renders the bacteria avirulent. Thus DsbA is a critical mediator of virulence and inhibitors may act as antivirulence agents. Biophysical screening has been employed to identify fragments that bind to DsbA from Escherichia coli. Elaboration of one of these fragments produced compounds that inhibit DsbA activity in vitro. In cell-based assays, the compounds inhibit bacterial motility, but have no effect on growth in liquid culture, which is consistent with selective inhibition of DsbA. Crystal structures of inhibitors bound to DsbA indicate that they bind adjacent to the active site. Together, the data suggest that DsbA may be amenable to the development of novel antibacterial compounds that act by inhibiting bacterial virulence.
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Affiliation(s)
- Luke A Adams
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052 (Australia) http://www.pharm.monash.edu.au
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38
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Yuan G, Gedeon NG, Jankins TC, Jones GB. Novel approaches for targeting the adenosine A2Areceptor. Expert Opin Drug Discov 2014; 10:63-80. [DOI: 10.1517/17460441.2015.971006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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39
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Abstract
Membrane proteins have always presented technical challenges for structural studies because of their requirement for a lipid environment. Multiple approaches exist including X-ray crystallography and electron microscopy that can give significant insights into their structure and function. However, nuclear magnetic resonance (NMR) is unique in that it offers the possibility of determining the structures of unmodified membrane proteins in their native environment of phospholipid bilayers under physiological conditions. Furthermore, NMR enables the characterization of the structure and dynamics of backbone and side chain sites of the proteins alone and in complexes with both small molecules and other biopolymers. The learning curve has been steep for the field as most initial studies were performed under non-native environments using modified proteins until ultimately progress in both techniques and instrumentation led to the possibility of examining unmodified membrane proteins in phospholipid bilayers under physiological conditions. This review aims to provide an overview of the development and application of NMR to membrane proteins. It highlights some of the most significant structural milestones that have been reached by NMR spectroscopy of membrane proteins, especially those accomplished with the proteins in phospholipid bilayer environments where they function.
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40
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Disulfide bond formation in prokaryotes: history, diversity and design. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1402-14. [PMID: 24576574 DOI: 10.1016/j.bbapap.2014.02.014] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/12/2014] [Accepted: 02/16/2014] [Indexed: 01/16/2023]
Abstract
The formation of structural disulfide bonds is essential for the function and stability of a great number of proteins, particularly those that are secreted. There exists a variety of dedicated cellular catalysts and pathways from archaea to humans that ensure the formation of native disulfide bonds. In this review we describe the initial discoveries of these pathways and report progress in recent years in our understanding of the diversity of these pathways in prokaryotes, including those newly discovered in some archaea. We will also discuss the various successful efforts to achieve laboratory-based evolution and design of synthetic disulfide bond formation machineries in the bacterium Escherichia coli. These latter studies have also led to new more general insights into the redox environment of the cytoplasm and bacterial cell envelope. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.
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41
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McMahon RM, Premkumar L, Martin JL. Four structural subclasses of the antivirulence drug target disulfide oxidoreductase DsbA provide a platform for design of subclass-specific inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1391-401. [PMID: 24487020 DOI: 10.1016/j.bbapap.2014.01.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/19/2013] [Accepted: 01/22/2014] [Indexed: 01/11/2023]
Abstract
By catalyzing oxidative protein folding, the bacterial disulfide bond protein A (DsbA) plays an essential role in the assembly of many virulence factors. Predictably, DsbA disruption affects multiple downstream effector molecules, resulting in pleiotropic effects on the virulence of important human pathogens. These findings mark DsbA as a master regulator of virulence, and identify the enzyme as a target for a new class of antivirulence agents that disarm pathogenic bacteria rather than killing them. The purpose of this article is to discuss and expand upon recent findings on DsbA and to provide additional novel insights into the druggability of this important disulfide oxidoreductase by comparing the structures and properties of 13 well-characterized DsbA enzymes. Our structural analysis involved comparison of the overall fold, the surface properties, the conformations of three loops contributing to the binding surface and the sequence identity of residues contributing to these loops. Two distinct structural classes were identified, classes I and II, which are differentiated by their central β-sheet arrangements and which roughly separate the DsbAs produced by Gram-negative from Gram-positive organisms. The classes can be further subdivided into a total of four subclasses on the basis of surface features. Class Ia is equivalent to the Enterobacteriaceae class that has been defined previously. Bioinformatic analyses support the classification of DsbAs into 3 of the 4 subclasses, but did not pick up the 4th subclass which is only apparent from analysis of DsbA electrostatic surface properties. In the context of inhibitor development, the discrete structural subclasses provide a platform for developing DsbA inhibitory scaffolds with a subclass-wide spectrum of activity. We expect that more DsbA classes are likely to be identified, as enzymes from other pathogens are explored, and we highlight the issues associated with structure-based inhibitor development targeting this pivotal mediator of bacterial virulence. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.
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Affiliation(s)
- Róisín M McMahon
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia.
| | - Lakshmanane Premkumar
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia.
| | - Jennifer L Martin
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia.
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42
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Walden PM, McMahon RM, Archbold JK. Membrane Protein Structures for Rational Antimicrobial Drug Design. Aust J Chem 2014. [DOI: 10.1071/ch14333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Antibiotic resistance is a major global health threat. Bacteria have developed novel resistance mechanisms to many of the latest generations of antibiotics and there is an urgent need to develop new therapies to combat these infections. Infections that are caused by multi-drug resistant Gram-negative bacteria result in poor prognosis, prolonged illness, and greater costs for health care. Recent research has pointed to several key bacterial membrane proteins as potential targets for drug and vaccine development. However, determination of the structures of these membrane proteins is not a trivial task. Here we review recent breakthroughs of the structural determination of bacterial membrane proteins and their potential for the future rational design of novel antimicrobial therapies.
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Lambruschini C, Veronesi M, Romeo E, Garau G, Bandiera T, Piomelli D, Scarpelli R, Dalvit C. Development of fragment-based n-FABS NMR screening applied to the membrane enzyme FAAH. Chembiochem 2013; 14:1611-9. [PMID: 23918626 DOI: 10.1002/cbic.201300347] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Indexed: 12/26/2022]
Abstract
Despite the recognized importance of membrane proteins as pharmaceutical targets, the reliable identification of fragment hits that are able to bind these proteins is still a major challenge. Among different ¹⁹F NMR spectroscopic methods, n-fluorine atoms for biochemical screening (n-FABS) is a highly sensitive technique that has been used efficiently for fragment screening, but its application for membrane enzymes has not been reported yet. Herein, we present the first successful application of n-FABS to the discovery of novel fragment hits, targeting the membrane-bound enzyme fatty acid amide hydrolase (FAAH), using a library of fluorinated fragments generated based on the different local environment of fluorine concept. The use of the recombinant fusion protein MBP-FAAH and the design of compound 11 as a suitable novel fluorinated substrate analogue allowed n-FABS screening to be efficiently performed using a very small amount of enzyme. Notably, we have identified 19 novel fragment hits that inhibit FAAH with a median effective concentration (IC₅₀) in the low mM-μM range. To the best of our knowledge, these results represent the first application of a ¹⁹F NMR fragment-based functional assay to a membrane protein.
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Affiliation(s)
- Chiara Lambruschini
- Department of Drug Discovery and Development, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova (Italy)
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Ksenia Guseva: Formation and Cooperative Behavior of Protein Complexes on the Cell Membrane. Cell Biochem Biophys 2013. [DOI: 10.1007/s12013-012-9420-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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45
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Barrett PJ, Chen J, Cho MK, Kim JH, Lu Z, Mathew S, Peng D, Song Y, Van Horn WD, Zhuang T, Sönnichsen FD, Sanders CR. The quiet renaissance of protein nuclear magnetic resonance. Biochemistry 2013; 52:1303-20. [PMID: 23368985 DOI: 10.1021/bi4000436] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
From roughly 1985 through the start of the new millennium, the cutting edge of solution protein nuclear magnetic resonance (NMR) spectroscopy was to a significant extent driven by the aspiration to determine structures. Here we survey recent advances in protein NMR that herald a renaissance in which a number of its most important applications reflect the broad problem-solving capability displayed by this method during its classical era during the 1970s and early 1980s.
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Affiliation(s)
- Paul J Barrett
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232-8725, United States
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Chen D, Errey JC, Heitman LH, Marshall FH, IJzerman AP, Siegal G. Fragment screening of GPCRs using biophysical methods: identification of ligands of the adenosine A(2A) receptor with novel biological activity. ACS Chem Biol 2012; 7:2064-73. [PMID: 23013674 DOI: 10.1021/cb300436c] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fragment-based drug discovery (FBDD) has proven a powerful method to develop novel drugs with excellent oral bioavailability against challenging pharmaceutical targets such as protein-protein interaction targets. Very recently the underlying biophysical techniques have begun to be successfully applied to membrane proteins. Here we show that novel, ligand efficient small molecules with a variety of biological activities can be found by screening a small fragment library using thermostabilized (StaR) G protein-coupled receptors (GPCRs) and target immobilized NMR screening (TINS). Detergent-solubilized StaR adenosine A(2A) receptor was immobilized with retention of functionality, and a screen of 531 fragments was performed. Hits from the screen were thoroughly characterized for biochemical activity using the wild-type receptor. Both orthosteric and allosteric modulatory activity has been demonstrated in biochemical validation assays. Allosteric activity was confirmed in cell-based functional assays. The validated fragment hits make excellent starting points for a subsequent hit-to-lead elaboration program.
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Affiliation(s)
- Dan Chen
- ZoBio BV, Leiden 2300RA, The Netherlands
| | - James C. Errey
- Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City,
Hertfordshire AL7 3AX, U.K
| | | | - Fiona H. Marshall
- Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City,
Hertfordshire AL7 3AX, U.K
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Walden PM, Heras B, Chen KE, Halili MA, Rimmer K, Sharma P, Scanlon MJ, Martin JL. The 1.2 Å resolution crystal structure of TcpG, the Vibrio cholerae DsbA disulfide-forming protein required for pilus and cholera-toxin production. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1290-302. [PMID: 22993083 DOI: 10.1107/s0907444912026388] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 06/11/2012] [Indexed: 11/10/2022]
Abstract
The enzyme TcpG is a periplasmic protein produced by the Gram-negative pathogen Vibrio cholerae. TcpG is essential for the production of ToxR-regulated proteins, including virulence-factor pilus proteins and cholera toxin, and is therefore a target for the development of a new class of anti-virulence drugs. Here, the 1.2 Å resolution crystal structure of TcpG is reported using a cryocooled crystal. This structure is compared with a previous crystal structure determined at 2.1 Å resolution from data measured at room temperature. The new crystal structure is the first DsbA crystal structure to be solved at a sufficiently high resolution to allow the inclusion of refined H atoms in the model. The redox properties of TcpG are also reported, allowing comparison of its oxidoreductase activity with those of other DSB proteins. One of the defining features of the Escherichia coli DsbA enzyme is its destabilizing disulfide, and this is also present in TcpG. The data presented here provide new insights into the structure and redox properties of this enzyme, showing that the binding mode identified between E. coli DsbB and DsbA is likely to be conserved in TcpG and that the β5-α7 loop near the proposed DsbB binding site is flexible, and suggesting that the tense oxidized conformation of TcpG may be the consequence of a short contact at the active site that is induced by disulfide formation and is relieved by reduction.
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Affiliation(s)
- Patricia M Walden
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
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Abstract
Drug discovery on membrane proteins is still a difficult task, despite the recognized importance of membrane proteins as drug targets. Here, we present an overview of NMR methods available for structure-based drug design on membrane proteins. NMR spectroscopy is capable of identifying potential binders in screening and defining their relative binding constants, binding stoichiometry, conformation in the binding pocket and the relative binding orientation for binders of different series. Examples are given in the review highlighting the potential of NMR spectroscopy for future progress in drug discovery on membrane proteins.
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Hao GF, Wang F, Li H, Zhu XL, Yang WC, Huang LS, Wu JW, Berry EA, Yang GF. Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex. J Am Chem Soc 2012; 134:11168-76. [PMID: 22690928 DOI: 10.1021/ja3001908] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A critical challenge to the fragment-based drug discovery (FBDD) is its low-throughput nature due to the necessity of biophysical method-based fragment screening. Herein, a method of pharmacophore-linked fragment virtual screening (PFVS) was successfully developed. Its application yielded the first picomolar-range Q(o) site inhibitors of the cytochrome bc(1) complex, an important membrane protein for drug and fungicide discovery. Compared with the original hit compound 4 (K(i) = 881.80 nM, porcine bc(1)), the most potent compound 4f displayed 20 507-fold improved binding affinity (K(i) = 43.00 pM). Compound 4f was proved to be a noncompetitive inhibitor with respect to the substrate cytochrome c, but a competitive inhibitor with respect to the substrate ubiquinol. Additionally, we determined the crystal structure of compound 4e (K(i) = 83.00 pM) bound to the chicken bc(1) at 2.70 Å resolution, providing a molecular basis for understanding its ultrapotency. To our knowledge, this study is the first application of the FBDD method in the discovery of picomolar inhibitors of a membrane protein. This work demonstrates that the novel PFVS approach is a high-throughput drug discovery method, independent of biophysical screening techniques.
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Affiliation(s)
- Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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Boyd SM, Turnbull AP, Walse B. Fragment library design considerations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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