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Le Huray KIP, Wang H, Sobott F, Kalli AC. Systematic simulation of the interactions of pleckstrin homology domains with membranes. SCIENCE ADVANCES 2022; 8:eabn6992. [PMID: 35857458 PMCID: PMC9258823 DOI: 10.1126/sciadv.abn6992] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Pleckstrin homology (PH) domains can recruit proteins to membranes by recognition of phosphatidylinositol phosphate (PIP) lipids. Several family members are linked to diseases including cancer. We report the systematic simulation of the interactions of 100 mammalian PH domains with PIP-containing membranes. The observed PIP interaction hotspots recapitulate crystallographic binding sites and reveal a number of insights: (i) The β1 and β2 strands and their connecting loop constitute the primary PIP interaction site but are typically supplemented by interactions at the β3-β4 and β5-β6 loops; (ii) we reveal exceptional cases such as the Exoc8 PH domain; (iii) PH domains adopt different membrane-bound orientations and induce clustering of anionic lipids; and (iv) beyond family-level insights, our dataset sheds new light on individual PH domains, e.g., by providing molecular detail of secondary PIP binding sites. This work provides a global view of PH domain/membrane association involving multivalent association with anionic lipids.
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Affiliation(s)
- Kyle I. P. Le Huray
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - He Wang
- School of Computing, University of Leeds, Leeds, UK
| | - Frank Sobott
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Antreas C. Kalli
- Astbury Centre for Structural and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
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Sidarovich A, Will CL, Anokhina MM, Ceballos J, Sievers S, Agafonov DE, Samatov T, Bao P, Kastner B, Urlaub H, Waldmann H, Lührmann R. Identification of a small molecule inhibitor that stalls splicing at an early step of spliceosome activation. eLife 2017; 6. [PMID: 28300534 PMCID: PMC5354520 DOI: 10.7554/elife.23533] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/26/2017] [Indexed: 11/13/2022] Open
Abstract
Small molecule inhibitors of pre-mRNA splicing are important tools for identifying new spliceosome assembly intermediates, allowing a finer dissection of spliceosome dynamics and function. Here, we identified a small molecule that inhibits human pre-mRNA splicing at an intermediate stage during conversion of pre-catalytic spliceosomal B complexes into activated Bact complexes. Characterization of the stalled complexes (designated B028) revealed that U4/U6 snRNP proteins are released during activation before the U6 Lsm and B-specific proteins, and before recruitment and/or stable incorporation of Prp19/CDC5L complex and other Bact complex proteins. The U2/U6 RNA network in B028 complexes differs from that of the Bact complex, consistent with the idea that the catalytic RNA core forms stepwise during the B to Bact transition and is likely stabilized by the Prp19/CDC5L complex and related proteins. Taken together, our data provide new insights into the RNP rearrangements and extensive exchange of proteins that occurs during spliceosome activation. DOI:http://dx.doi.org/10.7554/eLife.23533.001
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Affiliation(s)
- Anzhalika Sidarovich
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Maria M Anokhina
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Javier Ceballos
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sonja Sievers
- Compound Management and Screening Center, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dmitry E Agafonov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Timur Samatov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Penghui Bao
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Berthold Kastner
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute for Clinical Chemistry Göttingen, University Medical Center, Göttingen, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Linke P, Amaning K, Maschberger M, Vallee F, Steier V, Baaske P, Duhr S, Breitsprecher D, Rak A. An Automated Microscale Thermophoresis Screening Approach for Fragment-Based Lead Discovery. ACTA ACUST UNITED AC 2015; 21:414-21. [PMID: 26637553 PMCID: PMC4800460 DOI: 10.1177/1087057115618347] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/28/2015] [Indexed: 11/17/2022]
Abstract
Fragment-based lead discovery has proved to be an effective alternative to high-throughput screenings in identifying chemical matter that can be developed into robust lead compounds. The search for optimal combinations of biophysical techniques that can correctly and efficiently identify and quantify binding can be challenging due to the physicochemical properties of fragments. In order to minimize the time and costs of screening, optimal combinations of biophysical techniques with maximal information content, sensitivity, and robustness are needed. Here we describe an approach utilizing automated microscale thermophoresis (MST) affinity screening to identify fragments active against MEK1 kinase. MST identified multiple hits that were confirmed by X-ray crystallography but not detected by orthogonal methods. Furthermore, MST also provided information about ligand-induced aggregation and protein denaturation. The technique delivered a large number of binders while reducing experimentation time and sample consumption, demonstrating the potential of MST to execute and maximize the efficacy of fragment screening campaigns.
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Affiliation(s)
- Pawel Linke
- NanoTemper Technologies GmbH, Munich, Germany
| | - Kwame Amaning
- Sanofi R&D, Structure-Design-Informatics, Vitry sur Seine, France
| | | | - Francois Vallee
- Sanofi R&D, Structure-Design-Informatics, Vitry sur Seine, France
| | - Valerie Steier
- Sanofi R&D, Structure-Design-Informatics, Vitry sur Seine, France
| | | | - Stefan Duhr
- NanoTemper Technologies GmbH, Munich, Germany
| | | | - Alexey Rak
- Sanofi R&D, Structure-Design-Informatics, Vitry sur Seine, France
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Vonkova I, Saliba AE, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler K, Maeda K, Rybin V, van Noort V, Ellenberg J, Bork P, Gavin AC. Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains. Cell Rep 2015; 12:1519-30. [DOI: 10.1016/j.celrep.2015.07.054] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 06/30/2015] [Accepted: 07/27/2015] [Indexed: 10/23/2022] Open
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Gorai S, Bagdi PR, Borah R, Paul D, Santra MK, Khan AT, Manna D. Insights into the inhibitory mechanism of triazole-based small molecules on phosphatidylinositol-4,5-bisphosphate binding pleckstrin homology domain. Biochem Biophys Rep 2015; 2:75-86. [PMID: 29124147 PMCID: PMC5668642 DOI: 10.1016/j.bbrep.2015.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 12/11/2022] Open
Abstract
Background Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is an important regulator of several cellular processes and a precursor for other second messengers which are involved in cell signaling pathways. Signaling proteins preferably interact with PI(4,5)P2 through its pleckstrin homology (PH) domain. Efforts are underway to design small molecule-based antagonist, which can specifically inhibit the PI(4,5)P2/PH-domain interaction to establish an alternate strategy for the development of drug(s) for phosphoinositide signaling pathways. Methods Surface plasmon resonance, molecular docking, circular dichroism, competitive Förster resonance energy transfer, isothermal titration calorimetric analyses and liposome pull down assay were used. Results In this study, we employed 1,2,3-triazol-4-yl methanol containing small molecule (CIPs) as antagonists for PI(4,5)P2/PH-domain interaction and determined their inhibitory effect by using competitive-surface plasmon resonance analysis (IC50 ranges from 53 to 159 nM for PI(4,5)P2/PLCδ1-PH domain binding assay). We also used phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3], phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2], PI(4,5)P2 specific PH-domains to determine binding selectivity of the compounds. Various physicochemical analyses showed that the compounds have weak affect on fluidity of the model membrane but, strongly interact with the phospholipase C δ1 (PLCδ1)-PH domains. The 1,2,3-triazol-4-yl methanol moiety and nitro group of the compounds are essential for their exothermic interaction with the PH-domains. Potent compound can efficiently displace PLCδ1-PH domain from plasma membrane to cytosol in A549 cells. Conclusions Overall, our studies demonstrate that these compounds interact with the PIP-binding PH-domains and inhibit their membrane recruitment. General significance These results suggest specific but differential binding of these compounds to the PLCδ1-PH domain and emphasize the role of their structural differences in binding parameters. These triazole-based compounds could be directly used/further developed as potential inhibitor for PH domain-dependent enzyme activity.
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Affiliation(s)
- Sukhamoy Gorai
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Prasanta Ray Bagdi
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Rituparna Borah
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Debasish Paul
- National Center for Cell Science, Pune 411007, Maharashtra, India
| | | | - Abu Taleb Khan
- Alia University, DN 18, 8th Floor, Sector V, Kolkata 700091, India
| | - Debasis Manna
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India
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Lennarz S, Heider E, Blind M, Mayer G. An aptamer to the MAP kinase insert region. ACS Chem Biol 2015; 10:320-7. [PMID: 25184543 DOI: 10.1021/cb5005756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Targeting functional, non-catalytic domains of protein kinases or other proteins is an emerging field in chemical biology research. Non-ATP competitive kinase inhibitors allow for the investigation of active-site independent functions, e.g., the biological role of protein-protein interactions. These inhibitors also serve as a starting point for developing novel therapeutic strategies. However, the identification of such inhibitors by means of conventional low molecular weight compounds represents a great challenge in modern drug discovery. Employing the mitogen-activated protein (MAP) kinase Erk2, we show that RNA aptamers have the capacity to be a novel, promising class of protein kinase inhibitors that can be applied to target individual subdomains and block domain specific functions without affecting kinase activity per se.
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Affiliation(s)
- Sabine Lennarz
- Life and Medical Sciences Institute, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Elena Heider
- Life and Medical Sciences Institute, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Michael Blind
- Life and Medical Sciences Institute, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
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Gorai S, Paul S, Sankaran G, Borah R, Santra MK, Manna D. Inhibition of phosphatidylinositol-3,4,5-trisphosphate binding to the AKT pleckstrin homology domain by 4-amino-1,2,5-oxadiazole derivatives. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00260e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
4-Amino-1,2,5-oxadiazole derivatives has been developed as an inhibitor of AKT pleckstrin homology domain.
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Affiliation(s)
- Sukhamoy Gorai
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | - Saurav Paul
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | | | - Rituparna Borah
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | | | - Debasis Manna
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
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