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Donovan RL, Edwards TA, Judge A, Blom AW, Kunutsor SK, Whitehouse MR. Effects of recurrent intra-articular corticosteroid injections for osteoarthritis at 3 months and beyond: a systematic review and meta-analysis in comparison to other injectables. Osteoarthritis Cartilage 2022; 30:1658-1669. [PMID: 36108937 DOI: 10.1016/j.joca.2022.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/08/2022] [Accepted: 07/16/2022] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Intra-articular corticosteroid injections (IACIs) provide temporary symptom relief in osteoarthritis (OA). This meta-analysis investigated the effects of recurrent IACIs at 3 months and beyond. DESIGN We searched Medline, Embase and Cochrane from inception to January 2021 for randomised controlled trials (RCTs) of patients with OA who received recurrent IACIs compared with other injectables, placebo or no treatment (primary outcomes: pain, function). Mean differences (MDs) with 95% confidence intervals were reported. RESULTS Ten RCTs were included (eight knee OA (n = 763), two trapeziometacarpal OA (n = 121)). Patients received between 2 and 8 injections, varying by trial. Trials compared recurrent IACIs with hyaluronic acid (HA), platelet-rich plasma (PRP), saline or orgotein (follow-up 3-24 months). Greater improvements in pain, function and QoL at 3-24 months were noted for the comparators than with IACIs, with comparators demonstrating an equal or superior effect, or the intervention effect attenuated during follow-up. Recurrent IACIs demonstrated no benefits in pain or function over placebo at 12-24 months. No serious adverse events were recorded. No studies reported on time-to-future interventions, risk of future prosthetic joint infection or other adverse events associated with subsequent joint replacement. CONCLUSIONS Recurrent IACIs often provide inferior (or non-superior) symptom relief compared with other injectables (including placebo) at 3 months and beyond. Other injectables (HA, PRP) often yielded greater improvements in pain and function up to 24 months post-injection. Existing RCTs on recurrent IACIs lack sufficient follow-up data to assess disease progression and time-to-future interventions.
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Affiliation(s)
- R L Donovan
- Musculoskeletal Research Unit, University of Bristol, Level 1 Learning and Research Building, Southmead Hospital, Bristol, BS10 5NB, UK; North Bristol NHS Trust, Southmead Road, Bristol, BS10 5NB, UK.
| | - T A Edwards
- North Bristol NHS Trust, Southmead Road, Bristol, BS10 5NB, UK.
| | - A Judge
- Musculoskeletal Research Unit, University of Bristol, Level 1 Learning and Research Building, Southmead Hospital, Bristol, BS10 5NB, UK; National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK.
| | - A W Blom
- Musculoskeletal Research Unit, University of Bristol, Level 1 Learning and Research Building, Southmead Hospital, Bristol, BS10 5NB, UK; North Bristol NHS Trust, Southmead Road, Bristol, BS10 5NB, UK; National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK.
| | - S K Kunutsor
- Musculoskeletal Research Unit, University of Bristol, Level 1 Learning and Research Building, Southmead Hospital, Bristol, BS10 5NB, UK; National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK.
| | - M R Whitehouse
- Musculoskeletal Research Unit, University of Bristol, Level 1 Learning and Research Building, Southmead Hospital, Bristol, BS10 5NB, UK; North Bristol NHS Trust, Southmead Road, Bristol, BS10 5NB, UK; National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK.
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2
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Hopkins FR, Álvarez-Rodríguez B, Heath GR, Panayi K, Hover S, Edwards TA, Barr JN, Fontana J. The Native Orthobunyavirus Ribonucleoprotein Possesses a Helical Architecture. mBio 2022; 13:e0140522. [PMID: 35762594 PMCID: PMC9426602 DOI: 10.1128/mbio.01405-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Bunyavirales order is the largest group of negative-sense RNA viruses, containing many lethal human pathogens for which approved anti-infective measures are not available. The bunyavirus genome consists of multiple negative-sense RNA segments enwrapped by the virus-encoded nucleocapsid protein (NP), which together with the viral polymerase form ribonucleoproteins (RNPs). RNPs represent substrates for RNA synthesis and virion assembly, which require inherent flexibility, consistent with the appearance of RNPs spilled from virions. These observations have resulted in conflicting models describing the overall RNP architecture. Here, we purified RNPs from Bunyamwera virus (BUNV), the prototypical orthobunyavirus. The lengths of purified RNPs imaged by negative staining resulted in 3 populations of RNPs, suggesting that RNPs possess a consistent method of condensation. Employing microscopy approaches, we conclusively show that the NP portion of BUNV RNPs is helical. Furthermore, we present a pseudo-atomic model for this portion based on a cryo-electron microscopy average at 13 Å resolution, which allowed us to fit the BUNV NP crystal structure by molecular dynamics. This model was confirmed by NP mutagenesis using a mini-genome system. The model shows that adjacent NP monomers in the RNP chain interact laterally through flexible N- and C-terminal arms only, with no longitudinal helix-stabilizing interactions, thus providing a potential model for the molecular basis for RNP flexibility. Excessive RNase treatment disrupts native RNPs, suggesting that RNA was key in maintaining the RNP structure. Overall, this work will inform studies on bunyaviral RNP assembly, packaging, and RNA replication, and aid in future antiviral strategies. IMPORTANCE Bunyaviruses are emerging RNA viruses that cause significant disease and economic burden and for which vaccines or therapies approved for humans are not available. The bunyavirus genome is wrapped up by the nucleoprotein (NP) and interacts with the viral polymerase, forming a ribonucleoprotein (RNP). This is the only form of the genome active for viral replication and assembly. However, until now how NPs are organized within an RNP was not known for any orthobunyavirus. Here, we purified RNPs from the prototypical orthobunyavirus, Bunyamwera virus, and employed microscopy approaches to show that the NP portion of the RNP was helical. We then combined our helical average with the known structure of an NP monomer, generating a pseudo-atomic model of this region. This arrangement allowed the RNPs to be highly flexible, which was critical for several stages of the viral replication cycle, such as segment circularization.
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Affiliation(s)
- Francis R. Hopkins
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - Beatriz Álvarez-Rodríguez
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - George R. Heath
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - Kyriakoulla Panayi
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - Samantha Hover
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - Thomas A. Edwards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - John N. Barr
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
| | - Juan Fontana
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leedsgrid.9909.9, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leedsgrid.9909.9, Leeds, United Kingdom
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3
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Hóbor F, Hegedüs Z, Ibarra AA, Petrovicz VL, Bartlett GJ, Sessions RB, Wilson AJ, Edwards TA. Understanding p300-transcription factor interactions using sequence variation and hybridization. RSC Chem Biol 2022; 3:592-603. [PMID: 35656479 PMCID: PMC9092470 DOI: 10.1039/d2cb00026a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/10/2022] [Indexed: 11/21/2022] Open
Abstract
The hypoxic response is central to cell function and plays a significant role in the growth and survival of solid tumours. HIF-1 regulates the hypoxic response by activating over 100...
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Affiliation(s)
- Fruzsina Hóbor
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Amaurys Avila Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Vencel L Petrovicz
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Gail J Bartlett
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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4
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Hetherington K, Dutt S, Ibarra AA, Cawood EE, Hobor F, Woolfson DN, Edwards TA, Nelson A, Sessions RB, Wilson AJ. Towards optimizing peptide-based inhibitors of protein-protein interactions: predictive saturation variation scanning (PreSaVS). RSC Chem Biol 2021; 2:1474-1478. [PMID: 34704051 PMCID: PMC8495968 DOI: 10.1039/d1cb00137j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 07/30/2021] [Indexed: 12/21/2022] Open
Abstract
A simple-to-implement and experimentally validated computational workflow for sequence modification of peptide inhibitors of protein–protein interactions (PPIs) is described. An experimentally validated approach for in silico modification of peptide based protein–protein interaction inhibitors is described.![]()
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Affiliation(s)
- Kristina Hetherington
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Som Dutt
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Amaurys A Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
| | - Emma E Cawood
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Fruzsina Hobor
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Derek N Woolfson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK .,School of Chemistry, University of Bristol, Cantock's Close Bristol BS8 1TS UK.,BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Adam Nelson
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK .,BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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5
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Smith CEL, Whitehouse LLE, Poulter JA, Wilkinson Hewitt L, Nadat F, Jackson BR, Manfield IW, Edwards TA, Rodd HD, Inglehearn CF, Mighell AJ. A missense variant in specificity protein 6 (SP6) is associated with amelogenesis imperfecta. Hum Mol Genet 2021; 29:1417-1425. [PMID: 32167558 PMCID: PMC7268548 DOI: 10.1093/hmg/ddaa041] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 01/01/2023] Open
Abstract
Amelogenesis is the process of enamel formation. For amelogenesis to proceed, the cells of the inner enamel epithelium (IEE) must first proliferate and then differentiate into the enamel-producing ameloblasts. Amelogenesis imperfecta (AI) is a heterogeneous group of genetic conditions that result in defective or absent tooth enamel. We identified a 2 bp variant c.817_818GC>AA in SP6, the gene encoding the SP6 transcription factor, in a Caucasian family with autosomal dominant hypoplastic AI. The resulting missense protein change, p.(Ala273Lys), is predicted to alter a DNA-binding residue in the first of three zinc fingers. SP6 has been shown to be crucial to both proliferation of the IEE and to its differentiation into ameloblasts. SP6 has also been implicated as an AI candidate gene through its study in rodent models. We investigated the effect of the missense variant in SP6 (p.(Ala273Lys)) using surface plasmon resonance protein-DNA binding studies. We identified a potential SP6 binding motif in the AMBN proximal promoter sequence and showed that wild-type (WT) SP6 binds more strongly to it than the mutant protein. We hypothesize that SP6 variants may be a very rare cause of AI due to the critical roles of SP6 in development and that the relatively mild effect of the missense variant identified in this study is sufficient to affect amelogenesis causing AI, but not so severe as to be incompatible with life. We suggest that current AI cohorts, both with autosomal recessive and dominant disease, be screened for SP6 variants.
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Affiliation(s)
- Claire E L Smith
- Division of Molecular Medicine, Leeds Institute of Medical Research, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Laura L E Whitehouse
- School of Dentistry, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9LU, UK
| | - James A Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Laura Wilkinson Hewitt
- Protein Production Facility, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Fatima Nadat
- Protein Production Facility, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Brian R Jackson
- Protein Production Facility, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Iain W Manfield
- Centre for Biomolecular Interactions Technology Facility, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds LS2 9JT, UK
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Helen D Rodd
- Academic Unit of Oral Health Dentistry and Society, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK
| | - Chris F Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Alan J Mighell
- School of Dentistry, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9LU, UK
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6
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Celis S, Hobor F, James T, Bartlett GJ, Ibarra AA, Shoemark DK, Hegedüs Z, Hetherington K, Woolfson DN, Sessions RB, Edwards TA, Andrews DM, Nelson A, Wilson AJ. Query-guided protein-protein interaction inhibitor discovery. Chem Sci 2021; 12:4753-4762. [PMID: 34163731 PMCID: PMC8179539 DOI: 10.1039/d1sc00023c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 02/19/2021] [Indexed: 12/04/2022] Open
Abstract
Protein-protein interactions (PPIs) are central to biological mechanisms, and can serve as compelling targets for drug discovery. Yet, the discovery of small molecule inhibitors of PPIs remains challenging given the large and typically shallow topography of the interacting protein surfaces. Here, we describe a general approach to the discovery of orthosteric PPI inhibitors that mimic specific secondary protein structures. Initially, hot residues at protein-protein interfaces are identified in silico or from experimental data, and incorporated into secondary structure-based queries. Virtual libraries of small molecules are then shape-matched against the queries, and promising ligands docked to target proteins. The approach is exemplified experimentally using two unrelated PPIs that are mediated by an α-helix (p53/hDM2) and a β-strand (GKAP/SHANK1-PDZ). In each case, selective PPI inhibitors are discovered with low μM activity as determined by a combination of fluorescence anisotropy and 1H-15N HSQC experiments. In addition, hit expansion yields a series of PPI inhibitors with defined structure-activity relationships. It is envisaged that the generality of the approach will enable discovery of inhibitors of a wide range of unrelated secondary structure-mediated PPIs.
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Affiliation(s)
- Sergio Celis
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Fruzsina Hobor
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Thomas James
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Gail J Bartlett
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Amaurys A Ibarra
- School of Biochemistry, University of Bristol Medical Sciences Building, University Walk Bristol BS8 1TD UK
| | - Deborah K Shoemark
- School of Biochemistry, University of Bristol Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol Life Sciences Building, Tyndall Avenue Bristol BS8 1TQ UK
| | - Zsófia Hegedüs
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Kristina Hetherington
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol Life Sciences Building, Tyndall Avenue Bristol BS8 1TQ UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol Life Sciences Building, Tyndall Avenue Bristol BS8 1TQ UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - David M Andrews
- Early Oncology, AstraZeneca Hodgkin Building, Chesterford Research Campus, Saffron Walden Cambridge CB10 1XL UK
| | - Adam Nelson
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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7
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Hegedüs Z, Hóbor F, Shoemark DK, Celis S, Lian LY, Trinh CH, Sessions RB, Edwards TA, Wilson AJ. Identification of β-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation. Chem Sci 2021; 12:2286-2293. [PMID: 34163995 PMCID: PMC8179271 DOI: 10.1039/d0sc05694d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/01/2020] [Indexed: 12/26/2022] Open
Abstract
β-Strand mediated protein-protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.
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Affiliation(s)
- Zsófia Hegedüs
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Fruzsina Hóbor
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Deborah K Shoemark
- School of Biochemistry, Biomedical Sciences Building, University of Bristol Bristol BS8 1TD UK
| | - Sergio Celis
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Lu-Yun Lian
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool Liverpool L69 3BX UK
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Richard B Sessions
- School of Biochemistry, Biomedical Sciences Building, University of Bristol Bristol BS8 1TD UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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8
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Miles JA, Hobor F, Trinh CH, Taylor J, Tiede C, Rowell PR, Jackson BR, Nadat FA, Ramsahye P, Kyle HF, Wicky BIM, Clarke J, Tomlinson DC, Wilson AJ, Edwards TA. Selective Affimers Recognise the BCL-2 Family Proteins BCL-x L and MCL-1 through Noncanonical Structural Motifs*. Chembiochem 2021; 22:232-240. [PMID: 32961017 PMCID: PMC7821230 DOI: 10.1002/cbic.202000585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/17/2020] [Indexed: 12/26/2022]
Abstract
The BCL-2 family is a challenging group of proteins to target selectively due to sequence and structural homologies across the family. Selective ligands for the BCL-2 family regulators of apoptosis are useful as probes to understand cell biology and apoptotic signalling pathways, and as starting points for inhibitor design. We have used phage display to isolate Affimer reagents (non-antibody-binding proteins based on a conserved scaffold) to identify ligands for MCL-1, BCL-xL , BCL-2, BAK and BAX, then used multiple biophysical characterisation methods to probe the interactions. We established that purified Affimers elicit selective recognition of their target BCL-2 protein. For anti-apoptotic targets BCL-xL and MCL-1, competitive inhibition of their canonical protein-protein interactions is demonstrated. Co-crystal structures reveal an unprecedented mode of molecular recognition; where a BH3 helix is normally bound, flexible loops from the Affimer dock into the BH3 binding cleft. Moreover, the Affimers induce a change in the target proteins towards a desirable drug-bound-like conformation. These proof-of-concept studies indicate that Affimers could be used as alternative templates to inspire the design of selective BCL-2 family modulators and more generally other protein-protein interaction inhibitors.
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Affiliation(s)
- Jennifer A. Miles
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Fruzsina Hobor
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Chi H. Trinh
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - James Taylor
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Christian Tiede
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Philip R. Rowell
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Brian R. Jackson
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Protein Production FacilityUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Fatima A. Nadat
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Protein Production FacilityUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Pallavi Ramsahye
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Hannah F. Kyle
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Basile I. M. Wicky
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Jane Clarke
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Darren C. Tomlinson
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Thomas A. Edwards
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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9
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Hoste ACR, Ruiz T, Fernández-Pacheco P, Jiménez-Clavero MÁ, Djadjovski I, Moreno S, Brun A, Edwards TA, Barr JN, Rueda P, Sastre P. Development of a multiplex assay for antibody detection in serum against pathogens affecting ruminants. Transbound Emerg Dis 2020; 68:1229-1239. [PMID: 32767820 PMCID: PMC8246919 DOI: 10.1111/tbed.13776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/02/2020] [Accepted: 08/03/2020] [Indexed: 12/03/2022]
Abstract
Numerous infectious diseases impacting livestock impose an important economic burden and in some cases also represent a threat to humans and are classified as zoonoses. Some zoonotic diseases are transmitted by vectors and, due to complex environmental and socio‐economic factors, the distribution of many of these pathogens is changing, with increasing numbers being found in previously unaffected countries. Here, we developed a multiplex assay, based on a suspension microarray, able to detect specific antibodies to five important pathogens of livestock (three of them zoonotic) that are currently emerging in new geographical locations: Rift Valley fever virus (RVFV), Crimean‐Congo haemorrhagic fever virus (CCHFV), Schmallenberg virus (SBV), Bluetongue virus (BTV) and the bacteria complex Mycobacterium tuberculosis. Using the Luminex platform, polystyrene microspheres were coated with recombinant proteins from each of the five pathogens. The mix of microspheres was used for the simultaneous detection of antibodies against the five corresponding diseases affecting ruminants. The following panel of sera was included in the study: 50 sera from sheep experimentally infected with RVFV, 74 sera from calves and lambs vaccinated with SBV, 26 sera from cattle vaccinated with Mycobacterium bovis, 30 field sera from different species of ruminants infected with CCHFV and 88 calf sera infected with BTV. Finally, to determine its diagnostic specificity 220 field sera from Spanish farms free of the five diseases were assessed. All the sera were classified using commercial ELISAs specific for each disease, used in this study as the reference technique. The results showed the multiplex assay exhibited good performance characteristics with values of sensitivity ranging from 93% to 100% and of specificity ranging from 96% to 99% depending on the pathogen. This new tool allows the simultaneous detection of antibodies against five important pathogens, reducing the volume of sample needed and the time of analysis where these pathogens are usually tested individually.
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Affiliation(s)
- Alexis C R Hoste
- Eurofins-Inmunología y Genética Aplicada (Eurofins-INGENASA), Madrid, Spain.,School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Tamara Ruiz
- Eurofins-Inmunología y Genética Aplicada (Eurofins-INGENASA), Madrid, Spain
| | - Paloma Fernández-Pacheco
- Centro de Investigación en Sanidad Animal - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CISA), Valdeolmos, Spain
| | - Miguel Ángel Jiménez-Clavero
- Centro de Investigación en Sanidad Animal - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CISA), Valdeolmos, Spain
| | - Igor Djadjovski
- Faculty of Veterinary Medicine, University Ss. Cyril & Methodius, Skopje, North Macedonia
| | - Sandra Moreno
- Centro de Investigación en Sanidad Animal - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CISA), Valdeolmos, Spain
| | - Alejandro Brun
- Centro de Investigación en Sanidad Animal - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CISA), Valdeolmos, Spain
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - John N Barr
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Paloma Rueda
- Eurofins-Inmunología y Genética Aplicada (Eurofins-INGENASA), Madrid, Spain
| | - Patricia Sastre
- Eurofins-Inmunología y Genética Aplicada (Eurofins-INGENASA), Madrid, Spain
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10
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Nicholson D, Edwards TA, O'Neill AJ, Ranson NA. Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics. Structure 2020; 28:1087-1100.e3. [PMID: 32857965 PMCID: PMC7546915 DOI: 10.1016/j.str.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/06/2020] [Accepted: 08/07/2020] [Indexed: 12/19/2022]
Abstract
Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and tigecycline are among the limited arsenal of drugs available for treatment of such infections. We present high-resolution structures of the 70S ribosome from A. baumannii in complex with these antibiotics, as determined by cryoelectron microscopy. Comparison with the ribosomes of other bacteria reveals several unique structural features at functionally important sites, including around the exit of the polypeptide tunnel and the periphery of the subunit interface. The structures also reveal the mode and site of interaction of these drugs with the ribosome. This work paves the way for the design of new inhibitors of translation to address infections caused by MDR A. baumannii. Cryo-EM structures of the ribosome from the pathogenic bacteria A. baumannii Unique structural features compared with other bacterial ribosomes The site and mode of binding of amikacin and tigecycline to this ribosome A putative alternative tigecycline-binding site at the 50S central protuberance
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Affiliation(s)
- David Nicholson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Alex J O'Neill
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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11
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Hetherington K, Hegedus Z, Edwards TA, Sessions RB, Nelson A, Wilson AJ. Stapled Peptides as HIF-1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency. Chemistry 2020; 26:7638-7646. [PMID: 32307728 PMCID: PMC7318359 DOI: 10.1002/chem.202000417] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/13/2020] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions (PPIs) control virtually all cellular processes and have thus emerged as potential targets for development of molecular therapeutics. Peptide-based inhibitors of PPIs are attractive given that they offer recognition potency and selectivity features that are ideal for function, yet, they do not predominantly populate the bioactive conformation, frequently suffer from poor cellular uptake and are easily degraded, for example, by proteases. The constraint of peptides in a bioactive conformation has emerged as a promising strategy to mitigate against these liabilities. In this work, using peptides derived from hypoxia-inducible factor 1 (HIF-1α) together with dibromomaleimide stapling, we identify constrained peptide inhibitors of the HIF-1α/p300 interaction that are more potent than their unconstrained sequences. Contrary to expectation, the increased potency does not correlate with an increased population of an α-helical conformation in the unbound state as demonstrated by experimental circular dichroism analysis. Rather, the ability of the peptide to adopt a bioactive α-helical conformation in the p300 bound state is better supported in the constrained variant as demonstrated by molecular dynamics simulations and circular dichroism difference spectra.
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Affiliation(s)
- Kristina Hetherington
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Zsofia Hegedus
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Richard B. Sessions
- School of BiochemistryUniversity of BristolMedical Sciences Building, University WalkBristolBS8 1TDUK
- BrisSynBioUniversity of Bristol, Life Sciences BuildingTyndall AvenueBristolBS8 1TQUK
| | - Adam Nelson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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12
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Álvarez-Rodríguez B, Tiede C, Hoste ACR, Surtees RA, Trinh CH, Slack GS, Chamberlain J, Hewson R, Fresco A, Sastre P, Tomlinson DC, Millner PA, Edwards TA, Barr JN. Characterization and applications of a Crimean-Congo hemorrhagic fever virus nucleoprotein-specific Affimer: Inhibitory effects in viral replication and development of colorimetric diagnostic tests. PLoS Negl Trop Dis 2020; 14:e0008364. [PMID: 32492018 PMCID: PMC7295242 DOI: 10.1371/journal.pntd.0008364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/15/2020] [Accepted: 05/05/2020] [Indexed: 12/23/2022] Open
Abstract
Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) is one of the most widespread medically important arboviruses, causing human infections that result in mortality rates of up to 60%. We describe the selection of a high-affinity small protein (Affimer-NP) that binds specifically to the nucleoprotein (NP) of CCHFV. We demonstrate the interference of Affimer-NP in the RNA-binding function of CCHFV NP using fluorescence anisotropy, and its inhibitory effects on CCHFV gene expression in mammalian cells using a mini-genome system. Solution of the crystallographic structure of the complex formed by these two molecules at 2.84 Å resolution revealed the structural basis for this interference, with the Affimer-NP binding site positioned at the critical NP oligomerization interface. Finally, we validate the in vitro application of Affimer-NP for the development of enzyme-linked immunosorbent and lateral flow assays, presenting the first published point-of-care format test able to detect recombinant CCHFV NP in spiked human and animal sera.
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Affiliation(s)
| | - Christian Tiede
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Alexis C. R. Hoste
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- INGENASA, Inmunología y Genética Aplicada S.A., Madrid, Spain
| | - Rebecca A. Surtees
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Chi H. Trinh
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Gillian S. Slack
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - John Chamberlain
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Roger Hewson
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Alba Fresco
- INGENASA, Inmunología y Genética Aplicada S.A., Madrid, Spain
| | - Patricia Sastre
- INGENASA, Inmunología y Genética Aplicada S.A., Madrid, Spain
| | - Darren C. Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Paul A. Millner
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Thomas A. Edwards
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - John N. Barr
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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13
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Ibarra AA, Bartlett GJ, Hegedüs Z, Dutt S, Hobor F, Horner KA, Hetherington K, Spence K, Nelson A, Edwards TA, Woolfson DN, Sessions RB, Wilson AJ. Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces. ACS Chem Biol 2019; 14:2252-2263. [PMID: 31525028 PMCID: PMC6804253 DOI: 10.1021/acschembio.9b00560] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Protein–protein
interactions (PPIs) are vital to all biological
processes. These interactions are often dynamic, sometimes transient,
typically occur over large topographically shallow protein surfaces,
and can exhibit a broad range of affinities. Considerable progress
has been made in determining PPI structures. However, given the above
properties, understanding the key determinants of their thermodynamic
stability remains a challenge in chemical biology. An improved ability
to identify and engineer PPIs would advance understanding of biological
mechanisms and mutant phenotypes and also provide a firmer foundation
for inhibitor design. In silico prediction of PPI
hot-spot amino acids using computational alanine scanning (CAS) offers
a rapid approach for predicting key residues that drive protein–protein
association. This can be applied to all known PPI structures; however
there is a trade-off between throughput and accuracy. Here we describe
a comparative analysis of multiple CAS methods, which highlights effective
approaches to improve the accuracy of predicting hot-spot residues.
Alongside this, we introduce a new method, BUDE Alanine Scanning,
which can be applied to single structures from crystallography and
to structural ensembles from NMR or molecular dynamics data. The comparative
analyses facilitate accurate prediction of hot-spots that we validate
experimentally with three diverse targets: NOXA-B/MCL-1 (an α-helix-mediated
PPI), SIMS/SUMO, and GKAP/SHANK-PDZ (both β-strand-mediated
interactions). Finally, the approach is applied to the accurate prediction
of hot-spot residues at a topographically novel Affimer/BCL-xL protein–protein interface.
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Affiliation(s)
- Amaurys A. Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
| | - Gail J. Bartlett
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Zsöfia Hegedüs
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Som Dutt
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Fruzsina Hobor
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Katherine A. Horner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Kristina Hetherington
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Kirstin Spence
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Adam Nelson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
| | - Derek N. Woolfson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Richard B. Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Andrew J. Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, U.K
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14
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Davies K, Afrough B, Mankouri J, Hewson R, Edwards TA, Barr JN. Tula orthohantavirus nucleocapsid protein is cleaved in infected cells and may sequester activated caspase-3 during persistent infection to suppress apoptosis. J Gen Virol 2019; 100:1208-1221. [PMID: 31268416 DOI: 10.1099/jgv.0.001291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The family Hantaviridae mostly comprises rodent-borne segmented negative-sense RNA viruses, many of which are capable of causing devastating disease in humans. In contrast, hantavirus infection of rodent hosts results in a persistent and inapparent infection through their ability to evade immune detection and inhibit apoptosis. In this study, we used Tula hantavirus (TULV) to investigate the interplay between viral and host apoptotic responses during early, peak and persistent phases of virus infection in cell culture. Examination of early-phase TULV infection revealed that infected cells were refractory to apoptosis, as evidenced by the complete lack of cleaved caspase-3 (casp-3C) staining, whereas in non-infected bystander cells casp-3C was highly abundant. Interestingly, at later time points, casp-3C was abundant in infected cells, but the cells remained viable and able to continue shedding infectious virus, and together these observations were suggestive of a TULV-associated apoptotic block. To investigate this block, we viewed TULV-infected cells using laser scanning confocal and wide-field deconvolution microscopy, which revealed that TULV nucleocapsid protein (NP) colocalized with, and sequestered, casp-3C within cytoplasmic ultrastructures. Consistent with casp-3C colocalization, we showed for the first time that TULV NP was cleaved in cells and that TULV NP and casp-3C could be co-immunoprecipitated, suggesting that this interaction was stable and thus unlikely to be solely confined to NP binding as a substrate to the casp-3C active site. To account for these findings, we propose a novel mechanism by which TULV NP inhibits apoptosis by spatially sequestering casp-3C from its downstream apoptotic targets within the cytosol.
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Affiliation(s)
- Katherine Davies
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Babak Afrough
- National Infection Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - Jamel Mankouri
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Roger Hewson
- National Infection Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - John N Barr
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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15
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Fuller J, Surtees RA, Shaw AB, Álvarez-Rodríguez B, Slack GS, Bell-Sakyi L, Mankouri J, Edwards TA, Hewson R, Barr JN. Hazara nairovirus elicits differential induction of apoptosis and nucleocapsid protein cleavage in mammalian and tick cells. J Gen Virol 2019; 100:392-402. [PMID: 30720418 DOI: 10.1099/jgv.0.001211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Nairoviridae family within the Bunyavirales order comprise tick-borne segmented negative-sense RNA viruses that cause serious disease in a broad range of mammals, yet cause a latent and lifelong infection in tick hosts. An important member of this family is Crimean-Congo haemorrhagic fever virus (CCHFV), which is responsible for serious human disease that results in case fatality rates of up to 30 %, and which exhibits the most geographically broad distribution of any tick-borne virus. Here, we explored differences in the cellular response of both mammalian and tick cells to nairovirus infection using Hazara virus (HAZV), which is a close relative of CCHFV within the CCHFV serogroup. We show that HAZV infection of human-derived SW13 cells led to induction of apoptosis, evidenced by activation of cellular caspases 3, 7 and 9. This was followed by cleavage of the classical apoptosis marker poly ADP-ribose polymerase, as well as cellular genome fragmentation. In addition, we show that the HAZV nucleocapsid (N) protein was abundantly cleaved by caspase 3 in these mammalian cells at a conserved DQVD motif exposed at the tip of its arm domain, and that cleaved HAZV-N was subsequently packaged into nascent virions. However, in stark contrast, we show for the first time that nairovirus infection of cells of the tick vector failed to induce apoptosis, as evidenced by undetectable levels of cleaved caspases and lack of cleaved HAZV-N. Our findings reveal that nairoviruses elicit diametrically opposed cellular responses in mammalian and tick cells, which may influence the infection outcome in the respective hosts.
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Affiliation(s)
- J Fuller
- 1School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - R A Surtees
- 1School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
- ‡Present address: Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Seestrasse 10, Berlin, 13353, Germany
| | - A B Shaw
- 1School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - B Álvarez-Rodríguez
- 1School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - G S Slack
- 2National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Lesley Bell-Sakyi
- 3Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool Science Park IC2, Liverpool, L3 5RF, UK
| | - J Mankouri
- 1School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
- 4Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - T A Edwards
- 1School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
- 4Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - R Hewson
- 2National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - J N Barr
- 1School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
- 4Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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16
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Selvaraj M, Yegambaram K, Todd EJAA, Richard CA, Dods RL, Pangratiou GM, Trinh CH, Moul SL, Murphy JC, Mankouri J, Éléouët JF, Barr JN, Edwards TA. The Structure of the Human Respiratory Syncytial Virus M2-1 Protein Bound to the Interaction Domain of the Phosphoprotein P Defines the Orientation of the Complex. mBio 2018; 9:e01554-18. [PMID: 30425144 PMCID: PMC6234862 DOI: 10.1128/mbio.01554-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/02/2018] [Indexed: 01/09/2023] Open
Abstract
Human respiratory syncytial virus (HRSV) is a negative-stranded RNA virus that causes a globally prevalent respiratory infection, which can cause life-threatening illness, particularly in the young, elderly, and immunocompromised. HRSV multiplication depends on replication and transcription of the HRSV genes by the virus-encoded RNA-dependent RNA polymerase (RdRp). For replication, this complex comprises the phosphoprotein (P) and the large protein (L), whereas for transcription, the M2-1 protein is also required. M2-1 is recruited to the RdRp by interaction with P and also interacts with RNA at overlapping binding sites on the M2-1 surface, such that binding of these partners is mutually exclusive. The molecular basis for the transcriptional requirement of M2-1 is unclear, as is the consequence of competition between P and RNA for M2-1 binding, which is likely a critical step in the transcription mechanism. Here, we report the crystal structure at 2.4 Å of M2-1 bound to the P interaction domain, which comprises P residues 90 to 110. The P90-110 peptide is alpha helical, and its position on the surface of M2-1 defines the orientation of the three transcriptase components within the complex. The M2-1/P interface includes ionic, hydrophobic, and hydrogen bond interactions, and the critical contribution of these contacts to complex formation was assessed using a minigenome assay. The affinity of M2-1 for RNA and P ligands was quantified using fluorescence anisotropy, which showed high-affinity RNAs could outcompete P. This has important implications for the mechanism of transcription, particularly the events surrounding transcription termination and synthesis of poly(A) sequences.IMPORTANCE Human respiratory syncytial virus (HRSV) is a leading cause of respiratory illness, particularly in the young, elderly, and immunocompromised, and has also been linked to the development of asthma. HRSV replication depends on P and L, whereas transcription also requires M2-1. M2-1 interacts with P and RNA at overlapping binding sites; while these interactions are necessary for transcriptional activity, the mechanism of M2-1 action is unclear. To better understand HRSV transcription, we solved the crystal structure of M2-1 in complex with the minimal P interaction domain, revealing molecular details of the M2-1/P interface and defining the orientation of M2-1 within the tripartite complex. The M2-1/P interaction is relatively weak, suggesting high-affinity RNAs may displace M2-1 from the complex, providing the basis for a new model describing the role of M2-1 in transcription. Recently, the small molecules quercetin and cyclopamine have been used to validate M2-1 as a drug target.
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Affiliation(s)
- Muniyandi Selvaraj
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Kavestri Yegambaram
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Eleanor J A A Todd
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Charles-Adrien Richard
- Unité de Virologie et Immunologie Moléculaires (UR892), INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rachel L Dods
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Georgia M Pangratiou
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Chi H Trinh
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Sophie L Moul
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - James C Murphy
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Jamel Mankouri
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Jean-François Éléouët
- Unité de Virologie et Immunologie Moléculaires (UR892), INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - John N Barr
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
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17
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Burslem GM, Kyle HF, Nelson A, Edwards TA, Wilson AJ. Correction: Correction: Hypoxia inducible factor (HIF) as a model for studying inhibition of protein–protein interactions. Chem Sci 2018; 9:2010-2011. [PMID: 30289127 PMCID: PMC6144542 DOI: 10.1039/c8sc90024h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 01/18/2018] [Indexed: 11/21/2022] Open
Abstract
Correction for ‘Correction: Hypoxia inducible factor (HIF) as a model for studying inhibition of protein–protein interactions’ by George M. Burslem et al., Chem. Sci., 2017, 8, 5214–5215.
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Affiliation(s)
- George M. Burslem
- School of Chemistry
- University of Leeds
- Leeds LS2 9JT
- UK
- Astbury Centre for Structural Molecular Biology
| | - Hannah F. Kyle
- Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds LS2 9JT
- UK
- School of Molecular and Cellular Biology
| | - Adam Nelson
- School of Chemistry
- University of Leeds
- Leeds LS2 9JT
- UK
- Astbury Centre for Structural Molecular Biology
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds LS2 9JT
- UK
- School of Molecular and Cellular Biology
| | - Andrew J. Wilson
- School of Chemistry
- University of Leeds
- Leeds LS2 9JT
- UK
- Astbury Centre for Structural Molecular Biology
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18
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Abstract
Human respiratory syncytial virus (HRSV) is a non-segmented negative stranded RNA virus and is recognized as the most important viral agent of lower respiratory tract infection worldwide, responsible for up to 199,000 deaths each year. The only FDA-approved regime to prevent HRSV-mediated disease is pre-exposure administration of a humanized HRSV-specific monoclonal antibody, which although being effective, is not in widespread usage due to its cost. No HRSV vaccine exists and so there remains a strong need for alternative and complementary anti-HRSV therapies. The HRSV M2-1 protein is a transcription factor and represents an attractive target for the development of antiviral compounds, based on its essential role in the viral replication cycle. To this end, a detailed analysis of M2-1 structure and functions will aid in identifying rational targets for structure-based antiviral drug design that can be developed in future translational research. Here we present an overview of the current understanding of the structure and function of HRSV M2-1, drawing on additional information derived from its structural homologues from other related viruses.
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Affiliation(s)
- Selvaraj Muniyandi
- School of Molecular and Cellular Biology, and The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Georgia Pangratiou
- School of Molecular and Cellular Biology, and The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, and The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - John N Barr
- School of Molecular and Cellular Biology, and The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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19
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Burslem GM, Kyle HF, Nelson A, Edwards TA, Wilson AJ. Further Correction: Hypoxia inducible factor (HIF) as a model for studying inhibition of protein–protein interactions. Chem Sci 2018; 9:2008-2009. [PMID: 30288251 PMCID: PMC6144545 DOI: 10.1039/c8sc90023j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 01/18/2018] [Indexed: 11/21/2022] Open
Abstract
Correction for ‘Hypoxia inducible factor (HIF) as a model for studying inhibition of protein–protein interactions’ by George M. Burslem et al., Chem. Sci., 2017, 8, 4188–4202.
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Affiliation(s)
- George M. Burslem
- School of Chemistry
- University of Leeds
- Leeds LS2 9JT
- UK
- Astbury Centre for Structural Molecular Biology
| | - Hannah F. Kyle
- Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds LS2 9JT
- UK
- School of Molecular and Cellular Biology
| | - Adam Nelson
- School of Chemistry
- University of Leeds
- Leeds LS2 9JT
- UK
- Astbury Centre for Structural Molecular Biology
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds LS2 9JT
- UK
- School of Molecular and Cellular Biology
| | - Andrew J. Wilson
- School of Chemistry
- University of Leeds
- Leeds LS2 9JT
- UK
- Astbury Centre for Structural Molecular Biology
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20
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Hughes DJ, Tiede C, Penswick N, Tang AAS, Trinh CH, Mandal U, Zajac KZ, Gaule T, Howell G, Edwards TA, Duan J, Feyfant E, McPherson MJ, Tomlinson DC, Whitehouse A. Generation of specific inhibitors of SUMO-1- and SUMO-2/3-mediated protein-protein interactions using Affimer (Adhiron) technology. Sci Signal 2017; 10:10/505/eaaj2005. [PMID: 29138295 DOI: 10.1126/scisignal.aaj2005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Because protein-protein interactions underpin most biological processes, developing tools that target them to understand their function or to inform the development of therapeutics is an important task. SUMOylation is the posttranslational covalent attachment of proteins in the SUMO family (SUMO-1, SUMO-2, or SUMO-3), and it regulates numerous cellular pathways. SUMOylated proteins are recognized by proteins with SUMO-interaction motifs (SIMs) that facilitate noncovalent interactions with SUMO. We describe the use of the Affimer system of peptide display for the rapid isolation of synthetic binding proteins that inhibit SUMO-dependent protein-protein interactions mediated by SIMs both in vitro and in cells. Crucially, these synthetic proteins did not prevent SUMO conjugation either in vitro or in cell-based systems, enabling the specific analysis of SUMO-mediated protein-protein interactions. Furthermore, through structural analysis and molecular modeling, we explored the molecular mechanisms that may underlie their specificity in interfering with either SUMO-1-mediated interactions or interactions mediated by either SUMO-2 or SUMO-3. Not only will these reagents enable investigation of the biological roles of SUMOylation, but the Affimer technology used to generate these synthetic binding proteins could also be exploited to design or validate reagents or therapeutics that target other protein-protein interactions.
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Affiliation(s)
- David J Hughes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, UK
| | - Christian Tiede
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Natalie Penswick
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Anna Ah-San Tang
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Chi H Trinh
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Upasana Mandal
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Katarzyna Z Zajac
- BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thembaninskosi Gaule
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Gareth Howell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | | | | | - Michael J McPherson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Darren C Tomlinson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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21
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Burslem GM, Kyle HF, Nelson A, Edwards TA, Wilson AJ. Correction: Hypoxia inducible factor (HIF) as a model for studying inhibition of protein-protein interactions. Chem Sci 2017; 8:5214-5215. [PMID: 30294414 PMCID: PMC6156820 DOI: 10.1039/c7sc90030a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 05/16/2017] [Indexed: 11/21/2022] Open
Abstract
[This corrects the article DOI: 10.1039/C7SC00388A.].
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Affiliation(s)
- George M Burslem
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Hannah F Kyle
- Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,School of Molecular and Cellular Biology , Faculty of Biological Sciences , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Adam Nelson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,School of Molecular and Cellular Biology , Faculty of Biological Sciences , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
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22
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Burslem GM, Kyle HF, Nelson A, Edwards TA, Wilson AJ. Hypoxia inducible factor (HIF) as a model for studying inhibition of protein-protein interactions. Chem Sci 2017; 8:4188-4202. [PMID: 28878873 PMCID: PMC5576430 DOI: 10.1039/c7sc00388a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/31/2017] [Indexed: 12/21/2022] Open
Abstract
The state of the art in identifying protein–protein interaction inhibitors of hypoxia inducible factor – a promising target for anticancer drug design – is described.
The modulation of protein–protein interactions (PPIs) represents a major challenge in modern chemical biology. Current approaches (e.g. high-throughput screening, computer aided ligand design) are recognised as having limitations in terms of identification of hit matter. Considerable success has been achieved in terms of developing new approaches to PPI modulator discovery using the p53/hDM2 and Bcl-2 family of PPIs. However these important targets in oncology might be considered as “low-hanging-fruit”. Hypoxia inducible factor (HIF) is an emerging, but not yet fully validated target for cancer chemotherapy. Its role is to regulate the hypoxic response and it does so through a plethora of protein–protein interactions of varying topology, topography and complexity: its modulation represents an attractive approach to prevent development of new vasculature by hypoxic tumours.
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Affiliation(s)
- George M Burslem
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Hannah F Kyle
- Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,School of Molecular and Cellular Biology , Faculty of Biological Sciences , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Adam Nelson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,School of Molecular and Cellular Biology , Faculty of Biological Sciences , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
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23
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Abstract
BACKGROUND There is substantial evidence for the benefits of exercise training in people with multiple sclerosis (MS). These benefits, however, have primarily been established in the early, relapsing disease phase or are derived from heterogeneous MS samples (ie, relapsing and progressive MS). This makes it challenging to determine whether the consequences of exercise training are similar in the relapsing and progressive disease courses. The role of exercise training in progressive MS is far less clear. This study examined the potential role of exercise training in people with progressive MS. METHODS We review the current evidence from studies examining conventional exercise training modalities (eg, cycle ergometry) as well as specialized exercise training approaches (eg, functional electrical stimulation cycling) in samples involving exclusively individuals with progressive MS. RESULTS The evidence reviewed from nine trials provides preliminary support for the benefits of exercise training with regard to fitness, symptom, and quality of life outcomes in progressive MS, although these data are currently limited and at times conflicting. CONCLUSIONS Considering the prevalence of progressive MS (ie, 1 million people worldwide), the lack of effective treatment options, and the considerable frustration of researchers, clinicians, and patients, we believe that exercise training represents a viable therapeutic option worthy of further consideration. Future research should involve well-designed, randomized clinical trials with appropriate sample sizes and control conditions to establish the safety, feasibility, and therapeutic efficacy of exercise training in progressive MS.
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24
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Burslem GM, Kyle HF, Breeze AL, Edwards TA, Nelson A, Warriner SL, Wilson AJ. Towards "bionic" proteins: replacement of continuous sequences from HIF-1α with proteomimetics to create functional p300 binding HIF-1α mimics. Chem Commun (Camb) 2016; 52:5421-4. [PMID: 27009828 PMCID: PMC4843846 DOI: 10.1039/c6cc01812b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An extended sequence of α-amino acids in HIF-1α is replaced with a non-natural topographical mimic of an α-helix comprised from an aromatic oligoamide to reproduce its p300 recognition properties.
Using the HIF-1α transcription factor as a model, this manuscript illustrates how an extended sequence of α-amino acids in a polypeptide can be replaced with a non-natural topographical mimic of an α-helix comprised from an aromatic oligoamide. The resultant hybrid is capable of reproducing the molecular recognition profile of the p300 binding sequence of HIF-1α from which it is derived.
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Affiliation(s)
- George M Burslem
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK.
| | - Hannah F Kyle
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK. and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK. and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK and Discovery Sciences, AstraZeneca R&D, Alderley Park, Cheshire, SK10 4TG, UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK. and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Adam Nelson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK.
| | - Stuart L Warriner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK.
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK.
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25
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Haywood NJ, Wolny M, Rogers B, Trinh CH, Shuping Y, Edwards TA, Peckham M. Hypertrophic cardiomyopathy mutations in the calponin-homology domain of ACTN2 affect actin binding and cardiomyocyte Z-disc incorporation. Biochem J 2016; 473:2485-93. [PMID: 27287556 PMCID: PMC4980809 DOI: 10.1042/bcj20160421] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 06/06/2016] [Accepted: 06/09/2016] [Indexed: 11/17/2022]
Abstract
α-Actinin-2 (ACTN2) is the only muscle isoform of α-actinin expressed in cardiac muscle. Mutations in this protein have been implicated in mild to moderate forms of hypertrophic cardiomyopathy (HCM). We have investigated the effects of two mutations identified from HCM patients, A119T and G111V, on the secondary and tertiary structure of a purified actin binding domain (ABD) of ACTN2 by circular dichroism and X-ray crystallography, and show small but distinct changes for both mutations. We also find that both mutants have reduced F-actin binding affinity, although the differences are not significant. The full length mEos2 tagged protein expressed in adult cardiomyocytes shows that both mutations additionally affect Z-disc localization and dynamic behaviour. Overall, these two mutations have small effects on structure, function and behaviour, which may contribute to a mild phenotype for this disease.
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Affiliation(s)
- Natalie J Haywood
- Astbury Centre for Structural Molecular Biology and the School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Marcin Wolny
- Astbury Centre for Structural Molecular Biology and the School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Brendan Rogers
- Astbury Centre for Structural Molecular Biology and the School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology and the School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Yu Shuping
- Astbury Centre for Structural Molecular Biology and the School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology and the School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Michelle Peckham
- Astbury Centre for Structural Molecular Biology and the School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
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26
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Pilutti LA, Motl RW, Edwards TA, Wilund KR. Rationale and design of a randomized controlled clinical trial of functional electrical stimulation cycling in persons with severe multiple sclerosis. Contemp Clin Trials Commun 2016; 3:147-152. [PMID: 29736463 PMCID: PMC5935873 DOI: 10.1016/j.conctc.2016.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/27/2016] [Accepted: 05/11/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND This randomized controlled trial (RCT) will examine the efficacy of supervised functional electrical stimulation (FES) cycling on walking performance and physiological function among persons with multiple sclerosis (MS) with severe mobility disability. METHODS/DESIGN This RCT will recruit 16 persons with MS that require unilateral or bilateral assistance for ambulation (i.e., Expanded Disability Status Scale (EDSS) score = 6.0-6.5). Participants will be randomized to one of two conditions: supervised FES cycling or passive cycling. The FES cycling condition will involve mild electrical stimulation that will generate an activation pattern that results in cycling the leg ergometer. The passive cycling condition will not provide any electrical stimulation, rather the movement of the pedals will be controlled by the electrical motor. Both conditions will be delivered 3 days/week for the same duration, over 6 months. Primary outcomes will include walking performance assessed as walking speed, endurance, and agility. Secondary outcomes will include physiological function assessed as cardiorespiratory fitness, muscular strength, and balance. Assessments will take place at baseline, mid-point (3-months), and immediately following the intervention (6-months). DISCUSSION This study will lay the foundation for the design of a future RCT by: (1) providing effect sizes that can be included in a power analysis for optimal sample size estimation; and (2) identifying cardiorespiratory fitness, muscular strength, and balance (i.e., physiological function) as mechanisms for the beneficial effects of FES cycling on walking performance. This trial will provide important information on a novel exercise rehabilitation therapy for managing walking impairment in persons with severe MS.
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Affiliation(s)
- Lara A Pilutti
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, 906 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Robert W Motl
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, 906 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Thomas A Edwards
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, 906 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Kenneth R Wilund
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, 906 S. Goodwin Ave., Urbana, IL 61801, USA
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27
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Kyle HF, Wickson KF, Stott J, Burslem GM, Breeze AL, Tiede C, Tomlinson DC, Warriner SL, Nelson A, Wilson AJ, Edwards TA. Exploration of the HIF-1α/p300 interface using peptide and Adhiron phage display technologies. Mol Biosyst 2016; 11:2738-49. [PMID: 26135796 DOI: 10.1039/c5mb00284b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The HIF-1α/p300 protein-protein interaction plays a key role in tumor metabolism and thus represents a high value target for anticancer drug-development. Although several studies have identified inhibitor candidates using rationale design, more detailed understanding of the interaction and binding interface is necessary to inform development of superior inhibitors. In this work, we report a detailed biophysical analysis of the native interaction with both peptide and Adhiron phage display experiments to identify novel binding motifs and binding regions of the surface of p300 to inform future inhibitor design.
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Affiliation(s)
- Hannah F Kyle
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
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28
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Stevenson SR, Kamisugi Y, Trinh CH, Schmutz J, Jenkins JW, Grimwood J, Muchero W, Tuskan GA, Rensing SA, Lang D, Reski R, Melkonian M, Rothfels CJ, Li FW, Larsson A, Wong GKS, Edwards TA, Cuming AC. Genetic Analysis of Physcomitrella patens Identifies ABSCISIC ACID NON-RESPONSIVE, a Regulator of ABA Responses Unique to Basal Land Plants and Required for Desiccation Tolerance. Plant Cell 2016; 28:1310-27. [PMID: 27194706 PMCID: PMC4944411 DOI: 10.1105/tpc.16.00091] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/18/2016] [Accepted: 05/13/2016] [Indexed: 05/19/2023]
Abstract
The anatomically simple plants that first colonized land must have acquired molecular and biochemical adaptations to drought stress. Abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. We identified ABA nonresponsive mutants in the model bryophyte Physcomitrella patens and genotyped a segregating population to map and identify the ABA NON-RESPONSIVE (ANR) gene encoding a modular protein kinase comprising an N-terminal PAS domain, a central EDR domain, and a C-terminal MAPKKK-like domain. anr mutants fail to accumulate dehydration tolerance-associated gene products in response to drought, ABA, or osmotic stress and do not acquire ABA-dependent desiccation tolerance. The crystal structure of the PAS domain, determined to 1.7-Å resolution, shows a conserved PAS-fold that dimerizes through a weak dimerization interface. Targeted mutagenesis of a conserved tryptophan residue within the PAS domain generates plants with ABA nonresponsive growth and strongly attenuated ABA-responsive gene expression, whereas deleting this domain retains a fully ABA-responsive phenotype. ANR orthologs are found in early-diverging land plant lineages and aquatic algae but are absent from more recently diverged vascular plants. We propose that ANR genes represent an ancestral adaptation that enabled drought stress survival of the first terrestrial colonizers but were lost during land plant evolution.
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Affiliation(s)
- Sean R Stevenson
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Jerry W Jenkins
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Jane Grimwood
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Stefan A Rensing
- University of Marburg, Plant Cell Biology, D-35043 Marburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Daniel Lang
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Ralf Reski
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | | | - Carl J Rothfels
- Department of Integrative Biology, University of California, Berkeley California 94720-3140
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Anders Larsson
- Uppsala University, Systematic Biology, 752 36 Uppsala, Sweden
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada BGI-Shenzhen, Shenzhen 518083, China
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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Azzarito V, Rowell P, Barnard A, Edwards TA, Macdonald A, Warriner SL, Wilson AJ. Probing Protein Surfaces: QSAR Analysis with Helix Mimetics. Chembiochem 2016; 17:768-73. [PMID: 26690307 PMCID: PMC6591138 DOI: 10.1002/cbic.201500504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Indexed: 12/17/2022]
Abstract
α-Helix-mediated protein-protein interactions (PPIs) are important targets for small-molecule inhibition; however, generic approaches to inhibitor design are in their infancy and would benefit from QSAR analyses to rationalise the noncovalent basis of molecular recognition by designed ligands. Using a helix mimetic based on an oligoamide scaffold, we have exploited the power of a modular synthesis to access compounds that can readily be used to understand the noncovalent determinants of hDM2 recognition by this series of cell-active p53/hDM2 inhibitors.
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Affiliation(s)
- Valeria Azzarito
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Philip Rowell
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Anna Barnard
- Department of Chemistry, Imperial College London, London, London, SW7 2AZ, UK
- Institue of Chemical Biology, Imperial College London, London, SW7 2AZ, UK
| | - Thomas A Edwards
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andrew Macdonald
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Stuart L Warriner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
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Burslem GM, Kyle HF, Prabhakaran P, Breeze AL, Edwards TA, Warriner SL, Nelson A, Wilson AJ. Synthesis of highly functionalized oligobenzamide proteomimetic foldamers by late stage introduction of sensitive groups. Org Biomol Chem 2016; 14:3782-6. [PMID: 27005701 PMCID: PMC4839272 DOI: 10.1039/c6ob00078a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/14/2016] [Indexed: 12/26/2022]
Abstract
α-Helix proteomimetics represent an emerging class of ligands that can be used to inhibit an array of helix mediated protein-protein interactions. Within this class of inhibitor, aromatic oligobenzamide foldamers have been widely and successfully used. This manuscript describes alternative syntheses of these compounds that can be used to access mimetics that are challenging to synthesize using previously described methodologies, permitting access to compounds functionalized with multiple sensitive side chains and accelerated library assembly through late stage derivatisation.
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Affiliation(s)
- George M Burslem
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK
| | - Hannah F Kyle
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Panchami Prabhakaran
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK and Discovery Sciences, AstraZeneca R&D, Alderley Park, Cheshire, SK10 4TG, UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Stuart L Warriner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK
| | - Adam Nelson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK
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31
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Miles JA, Yeo DJ, Rowell P, Rodriguez-Marin S, Pask CM, Warriner SL, Edwards TA, Wilson AJ. Hydrocarbon constrained peptides - understanding preorganisation and binding affinity. Chem Sci 2016; 7:3694-3702. [PMID: 28970875 PMCID: PMC5618334 DOI: 10.1039/c5sc04048e] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 02/15/2016] [Indexed: 12/19/2022] Open
Abstract
The development of constrained peptides represents an emerging strategy to generate peptide based probes and hits for drug-discovery that address challenging protein-protein interactions (PPIs). In this manuscript we report on the use of a novel α-alkenylglycine derived amino acid to synthesise hydrocarbon constrained BH3-family sequences (BIM and BID). Our biophysical and structural analyses illustrate that whilst the introduction of the constraint increases the population of the bioactive α-helical conformation of the peptide in solution, it does not enhance the inhibitory potency against pro-apoptotic Bcl-xL and Mcl-1 PPIs. SPR analyses indicate binding occurs via an induced fit mechanism whilst X-ray analyses illustrate none of the key interactions between the helix and protein are disturbed. The behaviour derives from enthalpy-entropy compensation which may be considered in terms of the ground state energies of the unbound constrained and unconstrained peptides; this has implications for the design of preorganised peptides to target protein-protein interactions.
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Affiliation(s)
- Jennifer A Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - David J Yeo
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - Philip Rowell
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,School of Molecular and Cellular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Silvia Rodriguez-Marin
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - Christopher M Pask
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - Stuart L Warriner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,School of Molecular and Cellular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK .
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32
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Surtees R, Ariza A, Punch EK, Trinh CH, Dowall SD, Hewson R, Hiscox JA, Barr JN, Edwards TA. The crystal structure of the Hazara virus nucleocapsid protein. BMC Struct Biol 2015; 15:24. [PMID: 26715309 PMCID: PMC4696240 DOI: 10.1186/s12900-015-0051-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/23/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND Hazara virus (HAZV) is a member of the Bunyaviridae family of segmented negative stranded RNA viruses, and shares the same serogroup as Crimean-Congo haemorrhagic fever virus (CCHFV). CCHFV is responsible for fatal human disease with a mortality rate approaching 30 %, which has an increased recent incidence within southern Europe. There are no preventative or therapeutic treatments for CCHFV-mediated disease, and thus CCHFV is classified as a hazard group 4 pathogen. In contrast HAZV is not associated with serious human disease, although infection of interferon receptor knockout mice with either CCHFV or HAZV results in similar disease progression. To characterise further similarities between HAZV and CCHFV, and support the use of HAZV as a model for CCHFV infection, we investigated the structure of the HAZV nucleocapsid protein (N) and compared it to CCHFV N. N performs an essential role in the viral life cycle by encapsidating the viral RNA genome, and thus, N represents a potential therapeutic target. RESULTS We present the purification, crystallisation and crystal structure of HAZV N at 2.7 Å resolution. HAZV N was expressed as an N-terminal glutathione S-transferase (GST) fusion protein then purified using glutathione affinity chromatography followed by ion-exchange chromatography. HAZV N crystallised in the P212121 space group with unit cell parameters a = 64.99, b = 76.10, and c = 449.28 Å. HAZV N consists of a globular domain formed mostly of alpha helices derived from both the N- and C-termini, and an arm domain comprising two long alpha helices. HAZV N has a similar overall structure to CCHFV N, with their globular domains superposing with an RMSD = 0.70 Å, over 368 alpha carbons that share 59 % sequence identity. Four HAZV N monomers crystallised in the asymmetric unit, and their head-to-tail assembly reveals a potential interaction site between monomers. CONCLUSIONS The crystal structure of HAZV N reveals a close similarity to CCHFV N, supporting the use of HAZV as a model for CCHFV. Structural similarity between the N proteins should facilitate study of the CCHFV and HAZV replication cycles without the necessity of working under containment level 4 (CL-4) conditions.
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Affiliation(s)
- Rebecca Surtees
- Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK. .,School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Molecular and Structural Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Antonio Ariza
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Molecular and Structural Biology, University of Leeds, Leeds, LS2 9JT, UK. .,Present address: Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
| | - Emma K Punch
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Molecular and Structural Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Chi H Trinh
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Molecular and Structural Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Stuart D Dowall
- Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK.
| | - Roger Hewson
- Public Health England, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK.
| | - Julian A Hiscox
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Molecular and Structural Biology, University of Leeds, Leeds, LS2 9JT, UK. .,Present address: Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - John N Barr
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Molecular and Structural Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Molecular and Structural Biology, University of Leeds, Leeds, LS2 9JT, UK.
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33
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Barnard A, Long K, Martin HL, Miles JA, Edwards TA, Tomlinson DC, Macdonald A, Wilson AJ. Selective and Potent Proteomimetic Inhibitors of Intracellular Protein-Protein Interactions. Angew Chem Weinheim Bergstr Ger 2015; 127:3003-3008. [PMID: 26877561 PMCID: PMC4737265 DOI: 10.1002/ange.201410810] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/15/2014] [Indexed: 01/07/2023]
Abstract
Inhibition of protein-protein interactions (PPIs) represents a major challenge in chemical biology and drug discovery. α-Helix mediated PPIs may be amenable to modulation using generic chemotypes, termed "proteomimetics", which can be assembled in a modular manner to reproduce the vectoral presentation of key side chains found on a helical motif from one partner within the PPI. In this work, it is demonstrated that by using a library of N-alkylated aromatic oligoamide helix mimetics, potent helix mimetics which reproduce their biophysical binding selectivity in a cellular context can be identified.
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Affiliation(s)
- Anna Barnard
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
| | - Kérya Long
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
| | - Heather L. Martin
- Leeds Institute of Biomedical and Clinical Sciences, Wellcome Trust Brenner Building, University of Leeds, St. James's University Hospital, Leeds LS9 7TF (UK)
| | - Jennifer A. Miles
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
| | - Thomas A. Edwards
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
| | - Darren C. Tomlinson
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
| | - Andrew Macdonald
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
| | - Andrew J. Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
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34
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Barnard A, Long K, Martin HL, Miles JA, Edwards TA, Tomlinson DC, Macdonald A, Wilson AJ. Selective and potent proteomimetic inhibitors of intracellular protein-protein interactions. Angew Chem Int Ed Engl 2015; 54:2960-5. [PMID: 25651514 PMCID: PMC4506525 DOI: 10.1002/anie.201410810] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/15/2014] [Indexed: 12/30/2022]
Abstract
Inhibition of protein–protein interactions (PPIs) represents a major challenge in chemical biology and drug discovery. α-Helix mediated PPIs may be amenable to modulation using generic chemotypes, termed “proteomimetics”, which can be assembled in a modular manner to reproduce the vectoral presentation of key side chains found on a helical motif from one partner within the PPI. In this work, it is demonstrated that by using a library of N-alkylated aromatic oligoamide helix mimetics, potent helix mimetics which reproduce their biophysical binding selectivity in a cellular context can be identified.
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Affiliation(s)
- Anna Barnard
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK); Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK)
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35
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Azzarito V, Miles JA, Fisher J, Edwards TA, Warriner SL, Wilson AJ. Stereocontrolled protein surface recognition using chiral oligoamide proteomimetic foldamers. Chem Sci 2015; 6:2434-2443. [PMID: 29308155 PMCID: PMC5646261 DOI: 10.1039/c4sc03559c] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/29/2015] [Indexed: 12/26/2022] Open
Abstract
An oligoamide helix mimicking foldamer with well-defined conformation is shown to recognize its target protein hDM2 in a manner that depends upon the composition, spatial projection and stereochemistry of functional groups appended to the scaffold.
The development of foldamers capable of selective molecular recognition of solvent exposed protein surfaces represents an outstanding challenge in supramolecular chemical biology. Here we introduce an oligoamide foldamer with well-defined conformation that bears all the hallmarks of an information rich oligomer. Specifically, the foldamer recognizes its target protein hDM2 leading to inhibition of its protein–protein interaction with p53 in a manner that depends upon the composition, spatial projection and stereochemistry of functional groups appended to the scaffold. Most significantly, selective inhibition of p53/hDM2 can be achieved against four other targets and the selectivity for p53/hDM2 inhibition versus Mcl-1/NOXA-B inhibition is critically dependent upon the stereochemistry of the helix mimetic.
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Affiliation(s)
- Valeria Azzarito
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Jennifer A Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Julie Fisher
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
| | - Thomas A Edwards
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK.,School of Molecular and Cellular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Stuart L Warriner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
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Barnard A, Long K, Yeo DJ, Miles JA, Azzarito V, Burslem GM, Prabhakaran P, A. Edwards T, Wilson AJ. Orthogonal functionalisation of α-helix mimetics. Org Biomol Chem 2014; 12:6794-9. [PMID: 25065821 PMCID: PMC4157654 DOI: 10.1039/c4ob00915k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 07/07/2014] [Indexed: 12/26/2022]
Abstract
α-Helix mediated protein-protein interactions are of major therapeutic importance. As such, the design of inhibitors of this class of interaction is of significant interest. We present methodology to modify N-alkylated aromatic oligoamide α-helix mimetics using 'click' chemistry. The effect is shown to modulate the binding properties of a series of selective p53/hDM2 inhibitors.
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Affiliation(s)
- Anna Barnard
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
| | - Kérya Long
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
| | - David J. Yeo
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
| | - Jennifer A. Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
| | - Valeria Azzarito
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
| | - George M. Burslem
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
| | - Panchami Prabhakaran
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
| | - Thomas A. Edwards
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
- School of Molecular and Cellular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Andrew J. Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
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37
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Burslem GM, Kyle HF, Breeze AL, Edwards TA, Nelson A, Warriner SL, Wilson AJ. Small-molecule proteomimetic inhibitors of the HIF-1α-p300 protein-protein interaction. Chembiochem 2014; 15:1083-7. [PMID: 24782431 PMCID: PMC4159589 DOI: 10.1002/cbic.201400009] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Indexed: 11/29/2022]
Abstract
The therapeutically relevant hypoxia inducible factor HIF-1α–p300 protein–protein interaction can be orthosterically inhibited with α-helix mimetics based on an oligoamide scaffold that recapitulates essential features of the C-terminal helix of the HIF-1α C-TAD (C-terminal transactivation domain). Preliminary SAR studies demonstrated the important role of side-chain size and hydrophobicity/hydrophilicity in determining potency. These small molecules represent the first biophysically characterised HIF-1α–p300 PPI inhibitors and the first examples of small-molecule aromatic oligoamide helix mimetics to be shown to have a selective binding profile. Although the compounds were less potent than HIF-1α, the result is still remarkable in that the mimetic reproduces only three residues from the 42-residue HIF-1α C-TAD from which it is derived.
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Affiliation(s)
- George M Burslem
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK); Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT (UK)
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38
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Shepherd DA, Ariza A, Edwards TA, Barr JN, Stonehouse NJ, Ashcroft AE. Probing bunyavirus N protein oligomerisation using mass spectrometry. Rapid Commun Mass Spectrom 2014; 28:793-800. [PMID: 24573811 PMCID: PMC4377080 DOI: 10.1002/rcm.6841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/14/2014] [Accepted: 01/14/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE Bunyaviruses have become a major threat to both humans and livestock in Europe and the Americas. The nucleocapsid (N) protein of these viruses is key to the replication cycle and knowledge of the N oligomerisation state is central to understanding the viral lifecycle and for development of therapeutic strategies. METHODS Bunyamwera virus and Schmallenberg virus N proteins (BUNV-N and SBV-N) were expressed recombinantly in E. coli as hexahistidine-SUMO-tagged fusions, and the tag removed subsequently. Noncovalent nano-electrospray ionisation mass spectrometry was conducted in the presence and absence of short RNA oligonucleotides. Instrumental conditions were optimised for the transmission of intact protein complexes into the gas phase. The resulting protein-protein and protein-RNA complexes were identified and their stoichiometries verified by their mass. Collision-induced dissociation tandem mass spectrometry was used in cases of ambiguity. RESULTS Both BUNV-N and SBV-N proteins reassembled into N-RNA complexes in the presence of RNA; however, SBV-N formed a wider range of complexes with varying oligomeric states. The N:RNA oligomers observed were consistent with a model of assembly via stepwise addition of N proteins. Furthermore, upon mixing the two proteins in the presence of RNA no heteromeric complexes were observed, thus revealing insights into the specificity of oligomerisation. CONCLUSIONS Noncovalent mass spectrometry has provided the first detailed analysis of the co-populated oligomeric species formed by these important viral proteins and revealed insights into their assembly pathways. Using this technique has also enabled comparisons to be made between the two N proteins.
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Affiliation(s)
- Dale A Shepherd
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
| | - Antonio Ariza
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
| | - John N Barr
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
| | - Nicola J Stonehouse
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
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Prabhakaran P, Barnard A, Murphy NS, Kilner CA, Edwards TA, Wilson AJ. Aromatic Oligoamide Foldamers with a “Wet Edge” as Inhibitors of the α-Helix-Mediated p53-hDM2 Protein-Protein Interaction. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Ariza A, Tanner SJ, Walter CT, Dent KC, Shepherd DA, Wu W, Matthews SV, Hiscox JA, Green TJ, Luo M, Elliott RM, Fooks AR, Ashcroft AE, Stonehouse NJ, Ranson NA, Barr JN, Edwards TA. Nucleocapsid protein structures from orthobunyaviruses reveal insight into ribonucleoprotein architecture and RNA polymerization. Nucleic Acids Res 2013; 41:5912-26. [PMID: 23595147 PMCID: PMC3675483 DOI: 10.1093/nar/gkt268] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
All orthobunyaviruses possess three genome segments of single-stranded negative sense RNA that are encapsidated with the virus-encoded nucleocapsid (N) protein to form a ribonucleoprotein (RNP) complex, which is uncharacterized at high resolution. We report the crystal structure of both the Bunyamwera virus (BUNV) N–RNA complex and the unbound Schmallenberg virus (SBV) N protein, at resolutions of 3.20 and 2.75 Å, respectively. Both N proteins crystallized as ring-like tetramers and exhibit a high degree of structural similarity despite classification into different orthobunyavirus serogroups. The structures represent a new RNA-binding protein fold. BUNV N possesses a positively charged groove into which RNA is deeply sequestered, with the bases facing away from the solvent. This location is highly inaccessible, implying that RNA polymerization and other critical base pairing events in the virus life cycle require RNP disassembly. Mutational analysis of N protein supports a correlation between structure and function. Comparison between these crystal structures and electron microscopy images of both soluble tetramers and authentic RNPs suggests the N protein does not bind RNA as a repeating monomer; thus, it represents a newly described architecture for bunyavirus RNP assembly, with implications for many other segmented negative-strand RNA viruses.
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Affiliation(s)
- Antonio Ariza
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
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Long K, Edwards TA, Wilson AJ. Microwave assisted solid phase synthesis of highly functionalized N-alkylated oligobenzamide α-helix mimetics. Bioorg Med Chem 2012; 21:4034-40. [PMID: 23117175 DOI: 10.1016/j.bmc.2012.09.053] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/26/2012] [Indexed: 12/12/2022]
Abstract
Protein-protein interactions (PPIs) mediate cellular pathways and are implicated in numerous aberrant conditions. α-Helix mimetics-small molecules that reproduce the spatial projection of key residues from an α-helix involved in a PPI-are attractive generic templates for development of screening libraries, however library syntheses of α-helix mimetics with diverse functionality are less established. This manuscript describes the automated, microwave assisted solid phase synthesis based on one such scaffold; an N-alkylated oligobenzamide.
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Affiliation(s)
- Kérya Long
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
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Fuller JC, Jackson RM, Edwards TA, Wilson AJ, Shirts MR. Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable. PLoS One 2012; 7:e43253. [PMID: 22916232 PMCID: PMC3423354 DOI: 10.1371/journal.pone.0043253] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/18/2012] [Indexed: 12/04/2022] Open
Abstract
The design of novel α-helix mimetic inhibitors of protein-protein interactions is of interest to pharmaceuticals and chemical genetics researchers as these inhibitors provide a chemical scaffold presenting side chains in the same geometry as an α-helix. This conformational arrangement allows the design of high affinity inhibitors mimicking known peptide sequences binding specific protein substrates. We show that GAFF and AutoDock potentials do not properly capture the conformational preferences of α-helix mimetics based on arylamide oligomers and identify alternate parameters matching solution NMR data and suitable for molecular dynamics simulation of arylamide compounds. Results from both docking and molecular dynamics simulations are consistent with the arylamides binding in the p53 peptide binding pocket. Simulations of arylamides in the p53 binding pocket of hDM2 are consistent with binding, exhibiting similar structural dynamics in the pocket as simulations of known hDM2 binders Nutlin-2 and a benzodiazepinedione compound. Arylamide conformations converge towards the same region of the binding pocket on the 20 ns time scale, and most, though not all dihedrals in the binding pocket are well sampled on this timescale. We show that there are two putative classes of binding modes for arylamide compounds supported equally by the modeling evidence. In the first, the arylamide compound lies parallel to the observed p53 helix. In the second class, not previously identified or proposed, the arylamide compound lies anti-parallel to the p53 helix.
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Affiliation(s)
- Jonathan C. Fuller
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Richard M. Jackson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Andrew J. Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Michael R. Shirts
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
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Azzarito V, Prabhakaran P, Bartlett AI, Murphy NS, Hardie MJ, Kilner CA, Edwards TA, Warriner SL, Wilson AJ. 2-O-alkylated para-benzamide α-helix mimetics: the role of scaffold curvature. Org Biomol Chem 2012; 10:6469-72. [PMID: 22785578 DOI: 10.1039/c2ob26262b] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The design and synthesis of a new 2-O-alklyated benzamide α-helix mimetic is described. Comparison with regioisomeric 3-O-alkylated benzamides permits a preliminary evaluation of the role that mimetic curvature has in determining molecular recognition properties.
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Affiliation(s)
- Valeria Azzarito
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
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Prabhakaran P, Azzarito V, Jacobs T, Hardie MJ, Kilner CA, Edwards TA, Warriner SL, Wilson AJ. Conformational properties of O-alkylated benzamides. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.11.078] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Walden M, Jenkins HT, Edwards TA. Structure of the Drosophila melanogaster Rab6 GTPase at 1.4 Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:744-8. [PMID: 21795785 DOI: 10.1107/s1744309111017453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 05/09/2011] [Indexed: 11/10/2022]
Abstract
Rab6 is a small GTPase that belongs to the p21 Ras superfamily. It is involved in vesicle trafficking between the Golgi apparatus and endosomes/ER in eukaryotes. The GDP-bound inactive protein undergoes conformational changes when the nucleotide is exchanged to GTP, allowing Rab6 to interact with a variety of different effector proteins. To further understand how these changes affect downstream protein binding, the crystal structure of Rab6 from Drosophila melanogaster has been solved to 1.4 Å resolution, the highest resolution for a Rab6 structure to date. The crystals belonged to space group C2, with unit-cell parameters a=116.5, b=42.71, c=86.86 Å, α=90, β=133.12, γ=90°. The model was refined to an R factor of 14.5% and an Rfree of 17.3%.
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Affiliation(s)
- Miriam Walden
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
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46
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Sussner KM, Edwards TA, Thompson HS, Jandorf L, Kwate NO, Forman A, Brown K, Kapil-Pair N, Bovbjerg DH, Schwartz MD, Valdimarsdottir HB. Ethnic, racial and cultural identity and perceived benefits and barriers related to genetic testing for breast cancer among at-risk women of African descent in New York City. Public Health Genomics 2011; 14:356-70. [PMID: 21540561 DOI: 10.1159/000325263] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 02/09/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Due to disparities in the use of genetic services, there has been growing interest in examining beliefs and attitudes related to genetic testing for breast and/or ovarian cancer risk among women of African descent. However, to date, few studies have addressed critical cultural variations among this minority group and their influence on such beliefs and attitudes. METHODS We assessed ethnic, racial and cultural identity and examined their relationships with perceived benefits and barriers related to genetic testing for cancer risk in a sample of 160 women of African descent (49% self-identified African American, 39% Black-West Indian/Caribbean, 12% Black-Other) who met genetic risk criteria and were participating in a larger longitudinal study including the opportunity for free genetic counseling and testing in New York City. All participants completed the following previously validated measures: (a) the multi-group ethnic identity measure (including ethnic search and affirmation subscales) and other-group orientation for ethnic identity, (b) centrality to assess racial identity, and (c) Africentrism to measure cultural identity. Perceived benefits and barriers related to genetic testing included: (1) pros/advantages (including family-related pros), (2) cons/disadvantages (including family-related cons, stigma and confidentiality concerns), and (3) concerns about abuses of genetic testing. RESULTS In multivariate analyses, several ethnic identity elements showed significant, largely positive relationships to perceived benefits about genetic testing for breast and/or ovarian cancer risk, the exception being ethnic search, which was positively associated with cons/disadvantages, in general, and family-related cons/disadvantages. Racial identity (centrality) showed a significant association with confidentiality concerns. Cultural identity (Africentrism) was not related to perceived benefits and/or barriers. CONCLUSIONS Ethnic and racial identity may influence perceived benefits and barriers related to genetic testing for breast and/or ovarian cancer risk among at-risk women of African descent. Genetic counseling services may want to take into account these factors in the creation of culturally-appropriate services which best meet the needs of this heterogenous population.
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Affiliation(s)
- K M Sussner
- Division of Cancer Prevention and Control, Department of Oncological Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA.
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48
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Plante JP, Burnley T, Malkova B, Webb ME, Warriner SL, Edwards TA, Wilson AJ. Oligobenzamide proteomimetic inhibitors of the p53-hDM2 protein-protein interaction. Chem Commun (Camb) 2009:5091-3. [PMID: 20448956 PMCID: PMC2898631 DOI: 10.1039/b908207g] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 06/10/2009] [Indexed: 12/28/2022]
Abstract
Oligobenzamide inhibitors of the p53-hDM2 protein-protein interaction are described.
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Affiliation(s)
- Jeffrey P. Plante
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT. ; Fax: +44 (0)113 3431409; Tel: +44 (0)113 3436565
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
| | - Thomas Burnley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
| | - Barbora Malkova
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
| | - Michael E. Webb
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT. ; Fax: +44 (0)113 3431409; Tel: +44 (0)113 3436565
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
| | - Stuart L. Warriner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT. ; Fax: +44 (0)113 3431409; Tel: +44 (0)113 3436565
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
| | - Andrew J. Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT. ; Fax: +44 (0)113 3431409; Tel: +44 (0)113 3436565
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
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Gupta YK, Lee TH, Edwards TA, Escalante CR, Kadyrova LY, Wharton RP, Aggarwal AK. Co-occupancy of two Pumilio molecules on a single hunchback NRE. RNA 2009; 15:1029-35. [PMID: 19372537 PMCID: PMC2685510 DOI: 10.1261/rna.1327609] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Pumilio controls a number of processes in eukaryotes, including the translational repression of hunchback (hb) mRNA in early Drosophila embryos. The Pumilio Puf domain binds to a pair of 32 nucleotide (nt) Nanos response elements (NRE1 and NRE2) within the 3' untranslated region of hb mRNA. Despite the elucidation of structures of human Pumilio Puf domain in complex with hb RNA elements, the nature of hb mRNA recognition remains unclear. In particular, the site that mediates regulation in vivo is significantly larger than the 8-10-nt RNA elements bound to single Puf molecules in crystal structures. Here we present biophysical and biochemical data that partially resolve the paradox. We show that each NRE is composed of two binding sites (Box A and Box B) and that two Puf domains can co-occupy a single NRE. The Puf domains have a higher affinity for the 3' Box B site than the 5' Box A site; binding to the intact NRE appears to be cooperative (at least in some experiments). We suggest that the 2 Pumilio:1 NRE complex is the functional regulatory unit in vivo.
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Affiliation(s)
- Yogesh K Gupta
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York 10029, USA
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Stead MA, Trinh CH, Garnett JA, Carr SB, Baron AJ, Edwards TA, Wright SC. A Beta-Sheet Interaction Interface Directs the Tetramerisation of the Miz-1 POZ Domain. J Mol Biol 2007; 373:820-6. [PMID: 17880999 DOI: 10.1016/j.jmb.2007.08.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Revised: 08/05/2007] [Accepted: 08/10/2007] [Indexed: 11/30/2022]
Abstract
The POZ/BTB domain is an evolutionarily conserved motif found in approximately 40 zinc-finger transcription factors (POZ-ZF factors). Several POZ-ZF factors are implicated in human cancer, and POZ domain interaction interfaces represent an attractive target for therapeutic intervention. Miz-1 (Myc-interacting zinc-finger protein) is a POZ-ZF factor that regulates DNA-damage-induced cell cycle arrest and plays an important role in human cancer by virtue of its interaction with the c-Myc and BCL6 oncogene products. The Miz-1 POZ domain mediates both self-association and the recruitment of non-POZ partners. POZ-ZF factors generally function as homodimers, although higher-order associations and heteromeric interactions are known to be physiologically important; crucially, the interaction interfaces in such large complexes have not been characterised. We report here the crystal structure of the Miz-1 POZ domain up to 2.1 A resolution. The tetrameric organisation of Miz-1 POZ reveals two types of interaction interface between subunits; an interface of alpha-helices resembles the dimerisation interface of reported POZ domain structures, whereas a novel beta-sheet interface directs the association of two POZ domain dimers. We show that the beta-sheet interface directs the tetramerisation of the Miz-1 POZ domain in solution and therefore represents a newly described candidate interface for the higher-order homo- and hetero-oligomerisation of POZ-ZF proteins in vivo.
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Affiliation(s)
- Mark A Stead
- Molecular Cell Biology Research Group, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Garstang/Astbury Buildings, Leeds LS2 9JT, UK
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