1
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Tomlinson L, Batchelor M, Sarsby J, Byrne DP, Brownridge PJ, Bayliss R, Eyers PA, Eyers CE. Exploring the Conformational Landscape and Stability of Aurora A Using Ion-Mobility Mass Spectrometry and Molecular Modeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:420-435. [PMID: 35099954 PMCID: PMC9007459 DOI: 10.1021/jasms.1c00271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 05/06/2023]
Abstract
Protein kinase inhibitors are highly effective in treating diseases driven by aberrant kinase signaling and as chemical tools to help dissect the cellular roles of kinase signaling complexes. Evaluating the effects of binding of small molecule inhibitors on kinase conformational dynamics can assist in understanding both inhibition and resistance mechanisms. Using gas-phase ion-mobility mass spectrometry (IM-MS), we characterize changes in the conformational landscape and stability of the protein kinase Aurora A (Aur A) driven by binding of the physiological activator TPX2 or small molecule inhibition. Aided by molecular modeling, we establish three major conformations, the relative abundances of which were dependent on the Aur A activation status: one highly populated compact conformer similar to that observed in most crystal structures, a second highly populated conformer possessing a more open structure infrequently found in crystal structures, and an additional low-abundance conformer not currently represented in the protein databank. Notably, inhibitor binding induces more compact configurations of Aur A, as adopted by the unbound enzyme, with both IM-MS and modeling revealing inhibitor-mediated stabilization of active Aur A.
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Affiliation(s)
- Lauren
J. Tomlinson
- Centre
for Proteome Research, Department of Biochemistry & Systems Biology,
Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry & Systems Biology, Institute of Systems, Molecular
& Integrative Biology, University of
Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Matthew Batchelor
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Joscelyn Sarsby
- Centre
for Proteome Research, Department of Biochemistry & Systems Biology,
Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Dominic P. Byrne
- Department
of Biochemistry & Systems Biology, Institute of Systems, Molecular
& Integrative Biology, University of
Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Philip J. Brownridge
- Centre
for Proteome Research, Department of Biochemistry & Systems Biology,
Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Richard Bayliss
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Patrick A. Eyers
- Department
of Biochemistry & Systems Biology, Institute of Systems, Molecular
& Integrative Biology, University of
Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Claire E. Eyers
- Centre
for Proteome Research, Department of Biochemistry & Systems Biology,
Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry & Systems Biology, Institute of Systems, Molecular
& Integrative Biology, University of
Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
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2
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Fujiwara D, Mihara K, Takayama R, Nakamura Y, Ueda M, Tsumuraya T, Fujii I. Chemical Modification of Phage-Displayed Helix-Loop-Helix Peptides to Construct Kinase-Focused Libraries. Chembiochem 2021; 22:3406-3409. [PMID: 34605137 PMCID: PMC9297947 DOI: 10.1002/cbic.202100450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/01/2021] [Indexed: 11/11/2022]
Abstract
Conformationally constrained peptides hold promise as molecular tools in chemical biology and as a new modality in drug discovery. The construction and screening of a target‐focused library could be a promising approach for the generation of de novo ligands or inhibitors against target proteins. Here, we have prepared a protein kinase‐focused library by chemically modifying helix‐loop‐helix (HLH) peptides displayed on phage and subsequently tethered to adenosine. The library was screened against aurora kinase A (AurA). The selected HLH peptide Bip‐3 retained the α‐helical structure and bound to AurA with a KD value of 13.7 μM. Bip‐3 and the adenosine‐tethered peptide Bip‐3‐Adc provided IC50 values of 103 μM and 7.7 μM, respectively, suggesting that Bip‐3‐Adc bivalently inhibited AurA. In addition, the selectivity of Bip‐3‐Adc to several protein kinases was tested, and was highest against AurA. These results demonstrate that chemical modification can enable the construction of a kinase‐focused library of phage‐displayed HLH peptides.
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Affiliation(s)
- Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Kousuke Mihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ryo Takayama
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Yusuke Nakamura
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Mitsuhiro Ueda
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Takeshi Tsumuraya
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
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3
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Wang H, Dawber RS, Zhang P, Walko M, Wilson AJ, Wang X. Peptide-based inhibitors of protein-protein interactions: biophysical, structural and cellular consequences of introducing a constraint. Chem Sci 2021; 12:5977-5993. [PMID: 33995995 PMCID: PMC8098664 DOI: 10.1039/d1sc00165e] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/07/2021] [Indexed: 12/19/2022] Open
Abstract
Protein-protein interactions (PPIs) are implicated in the majority of cellular processes by enabling and regulating the function of individual proteins. Thus, PPIs represent high-value, but challenging targets for therapeutic intervention. The development of constrained peptides represents an emerging strategy to generate peptide-based PPI inhibitors, typically mediated by α-helices. The approach can confer significant benefits including enhanced affinity, stability and cellular penetration and is ingrained in the premise that pre-organization simultaneously pays the entropic cost of binding, prevents a peptide from adopting a protease compliant β-strand conformation and shields the hydrophilic amides from the hydrophobic membrane. This conceptual blueprint for the empirical design of peptide-based PPI inhibitors is an exciting and potentially lucrative way to effect successful PPI inhibitor drug-discovery. However, a plethora of more subtle effects may arise from the introduction of a constraint that include changes to binding dynamics, the mode of recognition and molecular properties. In this review, we summarise the influence of inserting constraints on biophysical, conformational, structural and cellular behaviour across a range of constraining chemistries and targets, to highlight the tremendous success that has been achieved with constrained peptides alongside emerging design opportunities and challenges.
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Affiliation(s)
- Hongshuang Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences 5625 Renmin St. Changchun 130022 Jilin China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University Nanjing 210023 Jiangsu China
| | - Robert S Dawber
- 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
| | - Peiyu Zhang
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Martin Walko
- 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
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences 5625 Renmin St. Changchun 130022 Jilin China
- Department of Applied Chemistry and Engineering, University of Science and Technology of China Hefei 230026 China
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4
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Horne WS, Grossmann TN. Proteomimetics as protein-inspired scaffolds with defined tertiary folding patterns. Nat Chem 2020; 12:331-337. [PMID: 32029906 DOI: 10.1038/s41557-020-0420-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022]
Abstract
Proteins have evolved as a variable platform that provides access to molecules with diverse shapes, sizes and functions. These features have inspired chemists for decades to seek artificial mimetics of proteins with improved or novel properties. Such work has focused primarily on small protein fragments, often isolated secondary structures; however, there has lately been a growing interest in the design of artificial molecules that mimic larger, more complex tertiary folds. In this Perspective, we define these agents as 'proteomimetics' and discuss the recent advances in the field. Proteomimetics can be divided into three categories: protein domains with side-chain functionality that alters the native linear-chain topology; protein domains in which the chemical composition of the polypeptide backbone has been partially altered; and protein-like folded architectures that are composed entirely of non-natural monomer units. We give an overview of these proteomimetic approaches and outline remaining challenges facing the field.
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Affiliation(s)
- W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, the Netherlands.
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5
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Huang DH, Jian J, Li S, Zhang Y, Liu LZ. TPX2 silencing exerts anti‑tumor effects on hepatocellular carcinoma by regulating the PI3K/AKT signaling pathway. Int J Mol Med 2019; 44:2113-2122. [PMID: 31638175 PMCID: PMC6844623 DOI: 10.3892/ijmm.2019.4371] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/11/2019] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the primary causes of cancer-associated deaths worldwide. Current treatment methods include surgical resection, chemotherapy and radiotherapy; however the curative rate remains low, thus novel treatments are required. The aim of the present study was to investigate the role of targeting protein for Xenopus kinesin-like protein 2 (TPX2) in the growth of HCC and its underlying molecular mechanism. Immunohistochemistry staining, reverse transcription-quantitative (RT-q)PCR and western blotting were used to detect the expression of TPX2 mRNA and protein in liver cancer tissue samples, adjacent normal liver tissue samples, and the HCC cell lines Huh7, Hep3B, PLC/PRF/5 and MHCC97-H. The recombinant plasmid pMagic4.1-shRNA-TPX2 was constructed and transfected into Huh7 and Hep3B HCC cells to silence TPX2 expression. The proliferation, apoptosis, migration and invasion of Huh7 cells and Hep3B cells were evaluated before and after TPX2 silencing. The mRNA and protein expression levels of multiple signaling pathway-associated genes were detected by RT-qPCR and western blotting. The expression levels of TPX2 mRNA and protein were significantly higher in HCC tissue samples compared with adjacent normal liver tissue sample. TPX2 mRNA and protein expression levels were detected in the different HCC cell lines. The recombinant plasmid pMagic4.1-shRNA-TPX2 was successfully transfected into Huh7 and Hep3B cells, resulting in TPX2 silencing. TPX2 knockdown significantly reduced cell proliferation, cell migration and cell invasion of Huh7 and Hep3B cells, whilst also increasing the rate of apoptosis in these cells. Following TPX2 silencing, the expression levels of PI3K, phospho-AKT, Bcl-2, c-Myc and Cyclin D1 were significantly decreased, whereas the expression levels of P21 and P27 were significantly increased. In conclusion, TPX2 may suppress the growth of HCC by regulating the PI3K/AKT signaling pathway and thus, TPX2 may be a potential target for the treatment of liver cancer.
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Affiliation(s)
- Dan-Hong Huang
- Department of Clinical Laboratory, Jiading District Central Hospital of Shanghai University of Medicine and Health Sciences, Shanghai 201800, P.R. China
| | - Jie Jian
- Department of Gastroenterology, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Shuang Li
- Department of Gastroenterology, Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330008, P.R. China
| | - Yan Zhang
- Department of Oncology, Jiading District Central Hospital of Shanghai University of Medicine and Health Sciences, Shanghai 201800, P.R. China
| | - Li-Zhen Liu
- Department of Oncology, Jiading District Central Hospital of Shanghai University of Medicine and Health Sciences, Shanghai 201800, P.R. China
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6
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Bakail M, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. Recognition of ASF1 by Using Hydrocarbon-Constrained Peptides. Chembiochem 2019; 20:891-895. [PMID: 30512234 PMCID: PMC6468270 DOI: 10.1002/cbic.201800633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Indexed: 12/20/2022]
Abstract
Inhibiting the histone H3-ASF1 (anti-silencing function 1) protein-protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α-helix-mediated PPI, constraining the key histone H3 helix (residues 118-135) is a strategy through which chemical probes might be elaborated to test this hypothesis. In this work, variant H3118-135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy-entropy compensation occurs.
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Affiliation(s)
- May Bakail
- Institute for Integrative Biology of the Cell (I2BC)IBITECSCEACNRSUniversité Paris–SudUniversité Paris–Saclay91198Gif-sur-Yvette CedexFrance
- Present address: Inserm, U1016Institut CochinCNRSUMR8104Université Paris Descartes27, rue du Faubourg Saint-Jacques75014ParisFrance
| | - Silvia Rodriguez‐Marin
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Zsófia Hegedüs
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Marie E. Perrin
- Institute for Integrative Biology of the Cell (I2BC)IBITECSCEACNRSUniversité Paris–SudUniversité Paris–Saclay91198Gif-sur-Yvette CedexFrance
| | - Françoise Ochsenbein
- Institute for Integrative Biology of the Cell (I2BC)IBITECSCEACNRSUniversité Paris–SudUniversité Paris–Saclay91198Gif-sur-Yvette CedexFrance
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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7
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Wu Y, Kaur A, Fowler E, Wiedmann MM, Young R, Galloway WRJD, Olsen L, Sore HF, Chattopadhyay A, Kwan TTL, Xu W, Walsh SJ, de Andrade P, Janecek M, Arumugam S, Itzhaki LS, Lau YH, Spring DR. Toolbox of Diverse Linkers for Navigating the Cellular Efficacy Landscape of Stapled Peptides. ACS Chem Biol 2019; 14:526-533. [PMID: 30702850 DOI: 10.1021/acschembio.9b00063] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Stapled peptides have great potential as modulators of protein-protein interactions (PPIs). However, there is a vast landscape of chemical features that can be varied for any given peptide, and identifying a set of features that maximizes cellular uptake and subsequent target engagement remains a key challenge. Herein, we present a systematic analysis of staple functionality on the peptide bioactivity landscape in cellular assays. Through application of a "toolbox" of diversified dialkynyl linkers to the stapling of MDM2-binding peptides via a double-click approach, we conducted a study of cellular uptake and p53 activation as a function of the linker. Minor changes in the linker motif and the specific pairing of linker with peptide sequence can lead to substantial differences in bioactivity, a finding which may have important design implications for peptide-based inhibitors of other PPIs. Given the complexity of the structure-activity relationships involved, the toolbox approach represents a generalizable strategy for optimization when progressing from in vitro binding assays to cellular efficacy studies.
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Affiliation(s)
- Yuteng Wu
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Amandeep Kaur
- European Molecular Biology Laboratory Australia Node for Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Elaine Fowler
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Mareike M Wiedmann
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Reginald Young
- School of Chemistry , The University of Sydney , Eastern Avenue , Sydney , NSW 2006 , Australia
| | - Warren R J D Galloway
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Lasse Olsen
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Hannah F Sore
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Anasuya Chattopadhyay
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , United Kingdom
| | - Terence T-L Kwan
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Wenshu Xu
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , United Kingdom
| | - Stephen J Walsh
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Peterson de Andrade
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Matej Janecek
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Senthil Arumugam
- European Molecular Biology Laboratory Australia Node for Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences , University of New South Wales , Sydney , NSW 2052 , Australia
| | - Laura S Itzhaki
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , United Kingdom
| | - Yu Heng Lau
- School of Chemistry , The University of Sydney , Eastern Avenue , Sydney , NSW 2006 , Australia
| | - David R Spring
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
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8
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Gilburt JAH, Girvan P, Blagg J, Ying L, Dodson CA. Ligand discrimination between active and inactive activation loop conformations of Aurora-A kinase is unmodified by phosphorylation. Chem Sci 2019; 10:4069-4076. [PMID: 31015948 PMCID: PMC6461105 DOI: 10.1039/c8sc03669a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/01/2019] [Indexed: 01/14/2023] Open
Abstract
Activation loop phosphorylation changes the position of equilibrium between DFG-in-like and DFG-out-like conformations but not the conformational preference of inhibitors.
Structure-based drug design is commonly used to guide the development of potent and specific enzyme inhibitors. Many enzymes – such as protein kinases – adopt multiple conformations, and conformational interconversion is expected to impact on the design of small molecule inhibitors. We measured the dynamic equilibrium between DFG-in-like active and DFG-out-like inactive conformations of the activation loop of unphosphorylated Aurora-A alone, in the presence of the activator TPX2, and in the presence of kinase inhibitors. The unphosphorylated kinase had a shorter residence time of the activation loop in the active conformation and a shift in the position of equilibrium towards the inactive conformation compared with phosphorylated kinase for all conditions measured. Ligand binding was associated with a change in the position of conformational equilibrium which was specific to each ligand and independent of the kinase phosphorylation state. As a consequence of this, the ability of a ligand to discriminate between active and inactive activation loop conformations was also independent of phosphorylation. Importantly, we discovered that the presence of multiple enzyme conformations can lead to a plateau in the overall ligand Kd, despite increasing affinity for the chosen target conformation, and modelled the conformational discrimination necessary for a conformation-promoting ligand.
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Affiliation(s)
- James A H Gilburt
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK
| | - Paul Girvan
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , 15 Cotswold Road , Sutton , Surrey SM2 5NG , UK
| | - Liming Ying
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK
| | - Charlotte A Dodson
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK.,Department of Pharmacy and Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK .
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9
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Ali AM, Atmaj J, Van Oosterwijk N, Groves MR, Dömling A. Stapled Peptides Inhibitors: A New Window for Target Drug Discovery. Comput Struct Biotechnol J 2019; 17:263-281. [PMID: 30867891 PMCID: PMC6396041 DOI: 10.1016/j.csbj.2019.01.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/11/2022] Open
Abstract
Protein-protein interaction (PPI) is a hot topic in clinical research as protein networking has a major impact in human disease. Such PPIs are potential drugs targets, leading to the need to inhibit/block specific PPIs. While small molecule inhibitors have had some success and reached clinical trials, they have generally failed to address the flat and large nature of PPI surfaces. As a result, larger biologics were developed for PPI surfaces and they have successfully targeted PPIs located outside the cell. However, biologics have low bioavailability and cannot reach intracellular targets. A novel class -hydrocarbon-stapled α-helical peptides that are synthetic mini-proteins locked into their bioactive structure through site-specific introduction of a chemical linker- has shown promise. Stapled peptides show an ability to inhibit intracellular PPIs that previously have been intractable with traditional small molecule or biologics, suggesting that they offer a novel therapeutic modality. In this review, we highlight what stapling adds to natural-mimicking peptides, describe the revolution of synthetic chemistry techniques and how current drug discovery approaches have been adapted to stabilize active peptide conformations, including ring-closing metathesis (RCM), lactamisation, cycloadditions and reversible reactions. We provide an overview on the available stapled peptide high-resolution structures in the protein data bank, with four selected structures discussed in details due to remarkable interactions of their staple with the target surface. We believe that stapled peptides are promising drug candidates and open the doors for peptide therapeutics to reach currently "undruggable" space.
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Affiliation(s)
| | | | | | | | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan1, 9700AD Groningen, the Netherlands
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10
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Panicker RC, Chattopadhaya S, Coyne AG, Srinivasan R. Allosteric Small-Molecule Serine/Threonine Kinase Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:253-278. [PMID: 31707707 DOI: 10.1007/978-981-13-8719-7_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deregulation of protein kinase activity has been linked to many diseases ranging from cancer to AIDS and neurodegenerative diseases. Not surprisingly, drugging the human kinome - the complete set of kinases encoded by the human genome - has been one of the major drug discovery pipelines. Majority of the approved clinical kinase inhibitors target the ATP binding site of kinases. However, the remarkable sequence and structural similarity of ATP binding pockets of kinases make selective inhibition of kinases a daunting task. To circumvent these issues, allosteric inhibitors that target sites other than the orthosteric ATP binding pocket have been developed. The structural diversity of the allosteric sites allows these inhibitors to have higher selectivity, lower toxicity and improved physiochemical properties and overcome drug resistance associated with the use of conventional kinase inhibitors. In this chapter, we will focus on the allosteric inhibitors of selected serine/threonine kinases, outline the benefits of using these inhibitors and discuss the challenges and future opportunities.
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Affiliation(s)
- Resmi C Panicker
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China
| | | | - Anthony G Coyne
- University Chemical Laboratory, University of Cambridge, Cambridge, UK
| | - Rajavel Srinivasan
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China.
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11
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Cui C, Zhou X, Zhang W, Qu Y, Ke X. Is β-Catenin a Druggable Target for Cancer Therapy? Trends Biochem Sci 2018; 43:623-634. [DOI: 10.1016/j.tibs.2018.06.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 06/02/2018] [Accepted: 06/03/2018] [Indexed: 01/09/2023]
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12
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Robertson NS, Spring DR. Using Peptidomimetics and Constrained Peptides as Valuable Tools for Inhibiting Protein⁻Protein Interactions. Molecules 2018; 23:molecules23040959. [PMID: 29671834 PMCID: PMC6017787 DOI: 10.3390/molecules23040959] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 02/07/2023] Open
Abstract
Protein–protein interactions (PPIs) are tremendously important for the function of many biological processes. However, because of the structure of many protein–protein interfaces (flat, featureless and relatively large), they have largely been overlooked as potential drug targets. In this review, we highlight the current tools used to study the molecular recognition of PPIs through the use of different peptidomimetics, from small molecules and scaffolds to peptides. Then, we focus on constrained peptides, and in particular, ways to constrain α-helices through stapling using both one- and two-component techniques.
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Affiliation(s)
- Naomi S Robertson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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Speltz TE, Danes JM, Stender JD, Frasor J, Moore TW. A Cell-Permeable Stapled Peptide Inhibitor of the Estrogen Receptor/Coactivator Interaction. ACS Chem Biol 2018; 13:676-684. [PMID: 29309722 DOI: 10.1021/acschembio.7b01016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We and others have proposed that coactivator binding inhibitors, which block the interaction of estrogen receptor and steroid receptor coactivators, may represent a potential class of new breast cancer therapeutics. The development of coactivator binding inhibitors has been limited, however, because many of the current molecules which are active in in vitro and biochemical assays are not active in cell-based assays. Our goal in this work was to prepare a coactivator binding inhibitor active in cellular models of breast cancer. To accomplish this, we used molecular dynamics simulations to convert a high-affinity stapled peptide with poor cell permeability into R4K1, a cell-penetrating stapled peptide. R4K1 displays high binding affinity for estrogen receptor α, inhibits the formation of estrogen receptor/coactivator complexes, and distributes throughout the cell with a high percentage of nuclear localization. R4K1 represses native gene transcription mediated by estrogen receptor α and inhibits proliferation of estradiol-stimulated MCF-7 cells. Using RNA-Seq, we demonstrate that almost all of the effects of R4K1 on global gene transcription are estrogen-receptor-associated. This chemical probe provides a significant proof-of-concept for preparing cell-permeable stapled peptide inhibitors of the estrogen receptor/coactivator interaction.
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Affiliation(s)
- Thomas E. Speltz
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, Illinois 60612, United States
| | - Jeanne M. Danes
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, 1835 W Polk St, Chicago, Illinois 60612, United States
| | - Joshua D. Stender
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Jonna Frasor
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, 1835 W Polk St, Chicago, Illinois 60612, United States
- University of Illinois Cancer Center, 1801 W Taylor St., Chicago, Illinois 60612, United States
| | - Terry W. Moore
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, Illinois 60612, United States
- University of Illinois Cancer Center, 1801 W Taylor St., Chicago, Illinois 60612, United States
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Hu X, He Y, Wu L, Hao Y, Wang Z, Zheng W. Novel all-hydrocarbon stapled p110α[E545K] peptides as blockers of the oncogenic p110α[E545K]-IRS1 interaction. Bioorg Med Chem Lett 2017; 27:5446-5449. [PMID: 29138025 DOI: 10.1016/j.bmcl.2017.10.076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 10/23/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
Abstract
To follow up on our recent discovery of the 18-amino acid all-hydrocarbon [i, i + 4]-stapled p110α[E545K] peptide 1 that was shown to potently block the intracellular p110α[E545K]-IRS1 interaction (a protein-protein interaction uniquely present in cancer cells expressing p110α[E545K]) and the growth of the xenograft tumors formed by cancers harboring this mutation, in the current study we prepared and examined six derivatives of 1, i.e. stapled peptides 2-A, 2-B, 3-A, 3-B, 4-A, 4-B. We found that 2-A, 2-B, 4-A, and 4-B had higher % α-helicity than 1; moreover, the enhanced % α-helicity also led to an enhanced proteolytic stability. When compared with 1, the structurally simplified 14-amino acid 4-A and 4-B were found to more potently deactivate the AKT phosphorylation at Ser473 in the p110α[E545K]-expressing colon cancer cells, whose activation was previously demonstrated by us to be specifically derived from the p110α[E545K]-IRS1 interaction. The preliminary findings from the current study have laid a foundation for future more extensive studies on the stapled p110α[E545K] peptides newly identified in the current study.
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Affiliation(s)
- Xiao Hu
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China
| | - Yanhua He
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China
| | - Liping Wu
- Department of Genetics & Genome Sciences and Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Yujun Hao
- Department of Genetics & Genome Sciences and Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Zhenghe Wang
- Department of Genetics & Genome Sciences and Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Weiping Zheng
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, PR China.
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Bayliss R, Burgess SG, McIntyre PJ. Switching Aurora-A kinase on and off at an allosteric site. FEBS J 2017; 284:2947-2954. [PMID: 28342286 DOI: 10.1111/febs.14069] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/09/2017] [Accepted: 03/23/2017] [Indexed: 12/20/2022]
Abstract
Protein kinases are central players in the regulation of cell cycle and signalling pathways. Their catalytic activities are strictly regulated through post-translational modifications and protein-protein interactions that control switching between inactive and active states. These states have been studied extensively using protein crystallography, although the dynamic nature of protein kinases makes it difficult to capture all relevant states. Here, we describe two recent structures of Aurora-A kinase that trap its active and inactive states. In both cases, Aurora-A is trapped through interaction with a synthetic protein, either a single-domain antibody that inhibits the kinase or a hydrocarbon-stapled peptide that activates the kinase. These structures show how the distinct synthetic proteins target the same allosteric pocket with opposing effects on activity. These studies pave the way for the development of tools to probe these allosteric mechanisms in cells.
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Affiliation(s)
- Richard Bayliss
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, UK
| | - Selena G Burgess
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, UK
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