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Bexkens ML, Martin OMF, van den Heuvel JM, Schmitz MGJ, Teusink B, Bakker BM, van Hellemond JJ, Haanstra JR, Walkinshaw MD, Tielens AGM. The unusual kinetics of lactate dehydrogenase of Schistosoma mansoni and their role in the rapid metabolic switch after penetration of the mammalian host. Int J Parasitol 2024:S0020-7519(24)00054-7. [PMID: 38492780 DOI: 10.1016/j.ijpara.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 01/24/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Lactate dehydrogenase (LDH) from Schistosoma mansoni has peculiar properties for a eukaryotic LDH. Schistosomal LDH (SmLDH) isolated from schistosomes, and the recombinantly expressed protein, are strongly inhibited by ATP, which is neutralized by fructose-1,6-bisphosphate (FBP). In the conserved FBP/anion binding site we identified two residues in SmLDH (Val187 and Tyr190) that differ from the conserved residues in LDHs of other eukaryotes, but are identical to conserved residues in FBP-sensitive prokaryotic LDHs. Three-dimensional (3D) models were generated to compare the structure of SmLDH with other LDHs. These models indicated that residues Val187, and especially Tyr190, play a crucial role in the interaction of FBP with the anion pocket of SmLDH. These 3D models of SmLDH are also consistent with a competitive model of SmLDH inhibition in which ATP (inhibitor) and FBP (activator) compete for binding in a well-defined anion pocket. The model of bound ATP predicts a distortion of the nearby key catalytic residue His195, resulting in enzyme inhibition. To investigate a possible physiological role of this allosteric regulation of LDH in schistosomes we made a kinetic model in which the allosteric regulation of the glycolytic enzymes can be varied. The model showed that inhibition of LDH by ATP prevents fermentation to lactate in the free-living stages in water and ensures complete oxidation via the Krebs cycle of the endogenous glycogen reserves. This mechanism of allosteric inhibition by ATP prevents the untimely depletion of these glycogen reserves, the only fuel of the free-living cercariae. Neutralization by FBP of this ATP inhibition of LDH prevents accumulation of glycolytic intermediates when S. mansoni schistosomula are confronted with the sudden large increase in glucose availability upon penetration of the final host. It appears that the LDH of S. mansoni is special and well suited to deal with the variations in glucose availability the parasite encounters during its life cycle.
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Affiliation(s)
- Michiel L Bexkens
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Olivier M F Martin
- Systems Biology Lab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jos M van den Heuvel
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Marion G J Schmitz
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Bas Teusink
- Systems Biology Lab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Barbara M Bakker
- Systems Biology Lab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jaap J van Hellemond
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Jurgen R Haanstra
- Systems Biology Lab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Malcolm D Walkinshaw
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Aloysius G M Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands; Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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2
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Nare Z, Moses T, Burgess K, Schnaufer A, Walkinshaw MD, Michels PAM. Metabolic insights into phosphofructokinase inhibition in bloodstream-form trypanosomes. Front Cell Infect Microbiol 2023; 13:1129791. [PMID: 36864883 PMCID: PMC9971811 DOI: 10.3389/fcimb.2023.1129791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/26/2023] [Indexed: 02/16/2023] Open
Abstract
Previously, we reported the development of novel small molecules that are potent inhibitors of the glycolytic enzyme phosphofructokinase (PFK) of Trypanosoma brucei and related protists responsible for serious diseases in humans and domestic animals. Cultured bloodstream-form trypanosomes, which are fully reliant on glycolysis for their ATP production, are rapidly killed at submicromolar concentrations of these compounds, which have no effect on the activity of human PFKs and human cells. Single-day oral dosing cures stage 1 human trypanosomiasis in an animal model. Here we analyze changes in the metabolome of cultured trypanosomes during the first hour after addition of a selected PFK inhibitor, CTCB405. The ATP level of T. brucei drops quickly followed by a partial increase. Already within the first five minutes after dosing, an increase is observed in the amount of fructose 6-phosphate, the metabolite just upstream of the PFK reaction, while intracellular levels of the downstream glycolytic metabolites phosphoenolpyruvate and pyruvate show an increase and decrease, respectively. Intriguingly, a decrease in the level of O-acetylcarnitine and an increase in the amount of L-carnitine were observed. Likely explanations for these metabolomic changes are provided based on existing knowledge of the trypanosome's compartmentalized metabolic network and kinetic properties of its enzymes. Other major changes in the metabolome concerned glycerophospholipids, however, there was no consistent pattern of increase or decrease upon treatment. CTCB405 treatment caused less prominent changes in the metabolome of bloodstream-form Trypanosoma congolense, a ruminant parasite. This agrees with the fact that it has a more elaborate glucose catabolic network with a considerably lower glucose consumption rate than bloodstream-form T. brucei.
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Affiliation(s)
- Zandile Nare
- Institute of Immunology and Infection Research, School of Biological Sciences, Ashworth Building, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tessa Moses
- EdinOmics, RRID:SCR_021838, Centre for Engineering Biology, School of Biological Sciences, CH Waddington Building, The University of Edinburgh, Edinburgh, United Kingdom
| | - Karl Burgess
- EdinOmics, RRID:SCR_021838, Centre for Engineering Biology, School of Biological Sciences, CH Waddington Building, The University of Edinburgh, Edinburgh, United Kingdom
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, CH Waddington Building, The University of Edinburgh, Edinburgh, United Kingdom
| | - Achim Schnaufer
- Institute of Immunology and Infection Research, School of Biological Sciences, Ashworth Building, The University of Edinburgh, Edinburgh, United Kingdom
| | - Malcolm D. Walkinshaw
- Wellcome Centre for Cell Biology, School of Biological Sciences, Michael Swann Building, The University of Edinburgh, Edinburgh, United Kingdom
| | - Paul A. M. Michels
- Wellcome Centre for Cell Biology, School of Biological Sciences, Michael Swann Building, The University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Paul A. M. Michels,
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3
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Hjortdal J, Griffin MD, Cadoux M, Armitage WJ, Bylesjo M, Gabhann PM, Murphy CC, Pleyer U, Tole D, Vabres B, Walkinshaw MD, Gourraud P, Karakachoff M, Brouard S, Degauque N. Peripheral blood immune cell profiling of acute corneal transplant rejection. Am J Transplant 2022; 22:2337-2347. [PMID: 35704290 PMCID: PMC9796948 DOI: 10.1111/ajt.17119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/15/2022] [Revised: 05/17/2022] [Accepted: 06/09/2022] [Indexed: 01/25/2023]
Abstract
Acute rejection (AR) of corneal transplants (CT) has a profound effect on subsequent graft survival but detailed immunological studies in human CT recipients are lacking. In this multi-site, cross-sectional study, clinical details and blood samples were collected from adults with clinically diagnosed AR of full-thickness (FT)-CT (n = 35) and posterior lamellar (PL)-CT (n = 21) along with Stable CT recipients (n = 177) and adults with non-transplanted corneal disease (n = 40). For those with AR, additional samples were collected 3 months later. Immune cell analysis was performed by whole-genome microarrays (whole blood) and high-dimensional multi-color flow cytometry (peripheral blood mononuclear cells). For both, no activation signature was identified within the B cell and T cell repertoire at the time of AR diagnosis. Nonetheless, in FT- but not PL-CT recipients, AR was associated with differences in B cell maturity and regulatory CD4+ T cell frequency compared to stable allografts. These data suggest that circulating B cell and T cell subpopulations may provide insights into the regulation of anti-donor immune response in human CT recipients with differing AR risk. Our results suggest that, in contrast to solid organ transplants, genetic or cellular assays of peripheral blood are unlikely to be clinically exploitable for prediction or diagnosis of AR.
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Affiliation(s)
- Jesper Hjortdal
- Department of OphthalmologyAarhus University HospitalAarhusDenmark,Department of Clinical MedicineAarhus UniversityAarhusDenmark
| | - Matthew D. Griffin
- Regenerative Medicine Institute (REMEDI) at CÚRAM SFI Centre for Research in Medical DevicesSchool of Medicine, National University of Ireland GalwayGalwayIreland
| | - Marion Cadoux
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064NantesFrance,CHU Nantes, Institut De Transplantation Urologie Néphrologie (ITUN)NantesFrance
| | - W. John Armitage
- Translational Health SciencesUniversity of BristolBristolUK,Tissue and Eye ServicesNHS Blood and TransplantBristolUK
| | - Max Bylesjo
- Fios Genomics Ltd, Nine Edinburgh BioquarterEdinburghUK
| | | | - Conor C. Murphy
- Royal Victoria Eye and Ear HospitalDublinIreland,Royal College of Surgeons in Ireland University of Medicine and Health SciencesDublinIreland
| | - Uwe Pleyer
- Department of OphthalmologyCharité University HospitalBerlinGermany
| | - Derek Tole
- University Hospitals Bristol NHS Foundations TrustBristol Eye HospitalBristolUK
| | - Bertrand Vabres
- Nantes Université, CHU Nantes, Service OphtalmologieNantesFrance
| | - Malcolm D. Walkinshaw
- Wellcome Centre for Cell Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Pierre‐Antoine Gourraud
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064NantesFrance,CHU Nantes, Institut De Transplantation Urologie Néphrologie (ITUN)NantesFrance,CHU de Nantes, INSERM, CIC 1413, Pôle Hospitalo‐Universitaire 11: Santé Publique, Clinique des donnéesNantesFrance
| | - Matilde Karakachoff
- CHU de Nantes, INSERM, CIC 1413, Pôle Hospitalo‐Universitaire 11: Santé Publique, Clinique des donnéesNantesFrance
| | - Sophie Brouard
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064NantesFrance,CHU Nantes, Institut De Transplantation Urologie Néphrologie (ITUN)NantesFrance
| | - Nicolas Degauque
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064NantesFrance,CHU Nantes, Institut De Transplantation Urologie Néphrologie (ITUN)NantesFrance
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4
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McNae IW, Kinkead J, Malik D, Yen LH, Walker MK, Swain C, Webster SP, Gray N, Fernandes PM, Myburgh E, Blackburn EA, Ritchie R, Austin C, Wear MA, Highton AJ, Keats AJ, Vong A, Dornan J, Mottram JC, Michels PAM, Pettit S, Walkinshaw MD. Fast acting allosteric phosphofructokinase inhibitors block trypanosome glycolysis and cure acute African trypanosomiasis in mice. Nat Commun 2021; 12:1052. [PMID: 33594070 PMCID: PMC7887271 DOI: 10.1038/s41467-021-21273-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 06/19/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
The parasitic protist Trypanosoma brucei is the causative agent of Human African Trypanosomiasis, also known as sleeping sickness. The parasite enters the blood via the bite of the tsetse fly where it is wholly reliant on glycolysis for the production of ATP. Glycolytic enzymes have been regarded as challenging drug targets because of their highly conserved active sites and phosphorylated substrates. We describe the development of novel small molecule allosteric inhibitors of trypanosome phosphofructokinase (PFK) that block the glycolytic pathway resulting in very fast parasite kill times with no inhibition of human PFKs. The compounds cross the blood brain barrier and single day oral dosing cures parasitaemia in a stage 1 animal model of human African trypanosomiasis. This study demonstrates that it is possible to target glycolysis and additionally shows how differences in allosteric mechanisms may allow the development of species-specific inhibitors to tackle a range of proliferative or infectious diseases.
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Affiliation(s)
- Iain W McNae
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - James Kinkead
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Divya Malik
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Li-Hsuan Yen
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Martin K Walker
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | | | - Scott P Webster
- Centre for Cardiovascular Science, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Nick Gray
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Peter M Fernandes
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Elmarie Myburgh
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Elizabeth A Blackburn
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Ryan Ritchie
- Institute of Infection Immunity and Inflammation, College of Medical Veterinary Life-Sciences, University of Glasgow, Glasgow, UK
| | - Carol Austin
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | - Martin A Wear
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Adrian J Highton
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | - Andrew J Keats
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | - Antonio Vong
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | - Jacqueline Dornan
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Paul A M Michels
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Simon Pettit
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK.
| | - Malcolm D Walkinshaw
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK.
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5
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Pinto Torres JE, Yuan M, Goossens J, Versées W, Caljon G, Michels PA, Walkinshaw MD, Magez S, Sterckx YGJ. Structural and kinetic characterization of Trypanosoma congolense pyruvate kinase. Mol Biochem Parasitol 2020; 236:111263. [PMID: 32084384 DOI: 10.1016/j.molbiopara.2020.111263] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 12/01/2019] [Revised: 01/13/2020] [Accepted: 01/29/2020] [Indexed: 11/18/2022]
Abstract
Trypanosoma are blood-borne parasites and are the causative agents of neglected tropical diseases (NTDs) affecting both humans and animals. These parasites mainly rely on glycolysis for their energy production within the mammalian host, which is why trypanosomal glycolytic enzymes have been pursued as interesting targets for the development of trypanocidal drugs. The structure-function relationships of pyruvate kinases (PYKs) from trypanosomatids (Trypanosoma and Leishmania) have been well-studied within this context. In this paper, we describe the structural and enzymatic characterization of PYK from T. congolense (TcoPYK), the main causative agent of Animal African Trypanosomosis (AAT), by employing a combination of enzymatic assays, thermal unfolding studies and X-ray crystallography.
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Affiliation(s)
- Joar Esteban Pinto Torres
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Meng Yuan
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Michael Swann Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Julie Goossens
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Paul A Michels
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Michael Swann Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Michael Swann Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Stefan Magez
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Ghent University Global Campus, Songdomunhwa-Ro 119, Yeonsu-Gu, 406-840 Incheon, South Korea
| | - Yann G-J Sterckx
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium.
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Juárez-Jiménez J, Gupta AA, Karunanithy G, Mey ASJS, Georgiou C, Ioannidis H, De Simone A, Barlow PN, Hulme AN, Walkinshaw MD, Baldwin AJ, Michel J. Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A. Chem Sci 2020; 11:2670-2680. [PMID: 34084326 PMCID: PMC8157532 DOI: 10.1039/c9sc04696h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 09/18/2019] [Accepted: 01/14/2020] [Indexed: 12/21/2022] Open
Abstract
Proteins need to interconvert between many conformations in order to function, many of which are formed transiently, and sparsely populated. Particularly when the lifetimes of these states approach the millisecond timescale, identifying the relevant structures and the mechanism by which they interconvert remains a tremendous challenge. Here we introduce a novel combination of accelerated MD (aMD) simulations and Markov state modelling (MSM) to explore these 'excited' conformational states. Applying this to the highly dynamic protein CypA, a protein involved in immune response and associated with HIV infection, we identify five principally populated conformational states and the atomistic mechanism by which they interconvert. A rational design strategy predicted that the mutant D66A should stabilise the minor conformations and substantially alter the dynamics, whereas the similar mutant H70A should leave the landscape broadly unchanged. These predictions are confirmed using CPMG and R1ρ solution state NMR measurements. By efficiently exploring functionally relevant, but sparsely populated conformations with millisecond lifetimes in silico, our aMD/MSM method has tremendous promise for the design of dynamic protein free energy landscapes for both protein engineering and drug discovery.
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Affiliation(s)
- Jordi Juárez-Jiménez
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Arun A Gupta
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Gogulan Karunanithy
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Antonia S J S Mey
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Charis Georgiou
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Harris Ioannidis
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Alessio De Simone
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Paul N Barlow
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Alison N Hulme
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Malcolm D Walkinshaw
- School of Biological Sciences Michael Swann Building, Max Born Crescent Edinburgh EH9 3BF UK
| | - Andrew J Baldwin
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Julien Michel
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
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Fernandes PM, Kinkead J, McNae IW, Vásquez-Valdivieso M, Wear MA, Michels PAM, Walkinshaw MD. Kinetic and structural studies of Trypanosoma and Leishmania phosphofructokinases show evolutionary divergence and identify AMP as a switch regulating glycolysis versus gluconeogenesis. FEBS J 2020; 287:2847-2861. [PMID: 31838765 PMCID: PMC7383607 DOI: 10.1111/febs.15177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/13/2019] [Accepted: 12/12/2019] [Indexed: 11/30/2022]
Abstract
Trypanosomatids possess glycosome organelles that contain much of the glycolytic machinery, including phosphofructokinase (PFK). We present kinetic and structural data for PFK from three human pathogenic trypanosomatids, illustrating intriguing differences that may reflect evolutionary adaptations to differing ecological niches. The activity of Leishmania PFK – to a much larger extent than Trypanosoma PFK – is reliant on AMP for activity regulation, with 1 mm AMP increasing the L. infantum PFK (LiPFK) kcat/K0.5F6P value by 10‐fold, compared to only a 1.3‐ and 1.4‐fold increase for T. cruzi and T. brucei PFK, respectively. We also show that Leishmania PFK melts at a significantly lower (> 15 °C) temperature than Trypanosoma PFKs and that addition of either AMP or ATP results in a marked stabilization of the protein. Sequence comparisons of Trypanosoma spp. and Leishmania spp. show that divergence of the two genera involved amino acid substitutions that occur in the enzyme’s ‘reaching arms’ and ‘embracing arms’ that determine tetramer stability. The dramatic effects of AMP on Leishmania activity compared with the Trypanosoma PFKs may be explained by differences between the T‐to‐R equilibria for the two families, with the low‐melting Leishmania PFK favouring the flexible inactive T‐state in the absence of AMP. Sequence comparisons along with the enzymatic and structural data presented here also suggest there was a loss of AMP‐dependent regulation in Trypanosoma species rather than gain of this characteristic in Leishmania species and that AMP acts as a key regulator in Leishmania governing the balance between glycolysis and gluconeogenesis.
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Affiliation(s)
- Peter M Fernandes
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - James Kinkead
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Iain W McNae
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Monserrat Vásquez-Valdivieso
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Martin A Wear
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Paul A M Michels
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
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8
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Wapeesittipan P, Mey ASJS, Walkinshaw MD, Michel J. Allosteric effects in cyclophilin mutants may be explained by changes in nano-microsecond time scale motions. Commun Chem 2019. [DOI: 10.1038/s42004-019-0136-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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9
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De Simone A, Georgiou C, Ioannidis H, Gupta AA, Juárez-Jiménez J, Doughty-Shenton D, Blackburn EA, Wear MA, Richards JP, Barlow PN, Carragher N, Walkinshaw MD, Hulme AN, Michel J. A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors. Chem Sci 2019; 10:542-547. [PMID: 30746096 PMCID: PMC6335623 DOI: 10.1039/c8sc03831g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 08/27/2018] [Accepted: 10/14/2018] [Indexed: 12/27/2022] Open
Abstract
Cyclophilins (Cyps) are a major family of drug targets that are challenging to prosecute with small molecules because the shallow nature and high degree of conservation of the active site across human isoforms offers limited opportunities for potent and selective inhibition. Herein a computational approach based on molecular dynamics simulations and free energy calculations was combined with biophysical assays and X-ray crystallography to explore a flip in the binding mode of a reported urea-based Cyp inhibitor. This approach enabled access to a distal pocket that is poorly conserved among key Cyp isoforms, and led to the discovery of a new family of sub-micromolar cell-active inhibitors that offer unprecedented opportunities for the development of next-generation drug therapies based on Cyp inhibition. The computational approach is applicable to a broad range of organic functional groups and could prove widely enabling in molecular design.
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Affiliation(s)
- Alessio De Simone
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Charis Georgiou
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Harris Ioannidis
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Arun A Gupta
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Jordi Juárez-Jiménez
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Dahlia Doughty-Shenton
- Edinburgh Phenotypic Assay Centre , University of Edinburgh , Queen's Medical Research Institute , Little France Cres , Edinburgh , Scotland EH16 4TJ , UK
| | - Elizabeth A Blackburn
- The Edinburgh Protein Production Facility (EPPF) , University of Edinburgh , Level 3 Michael Swann Building, King's Buildings, Max Born Crescent , Edinburgh , Scotland EH9 3BF , UK
| | - Martin A Wear
- The Edinburgh Protein Production Facility (EPPF) , University of Edinburgh , Level 3 Michael Swann Building, King's Buildings, Max Born Crescent , Edinburgh , Scotland EH9 3BF , UK
| | - Jonathan P Richards
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Paul N Barlow
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Neil Carragher
- Cancer Research UK Edinburgh Centre , University of Edinburgh , MRC Institute of Genetics and Molecular Medicine , Crewe Road South , Edinburgh , Scotland EH4 2XR , UK
| | - Malcolm D Walkinshaw
- University of Edinburgh , Michael Swann Building, Max Born Crescent , Edinburgh , Scotland EH9 3BF , UK
| | - Alison N Hulme
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
| | - Julien Michel
- University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK .
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10
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Rojas F, Silvester E, Young J, Milne R, Tettey M, Houston DR, Walkinshaw MD, Pérez-Pi I, Auer M, Denton H, Smith TK, Thompson J, Matthews KR. Oligopeptide Signaling through TbGPR89 Drives Trypanosome Quorum Sensing. Cell 2018; 176:306-317.e16. [PMID: 30503212 PMCID: PMC6333907 DOI: 10.1016/j.cell.2018.10.041] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [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: 03/26/2018] [Revised: 09/13/2018] [Accepted: 10/17/2018] [Indexed: 02/03/2023]
Abstract
Trypanosome parasites control their virulence and spread by using quorum sensing (QS) to generate transmissible “stumpy forms” in their host bloodstream. However, the QS signal “stumpy induction factor” (SIF) and its reception mechanism are unknown. Although trypanosomes lack G protein-coupled receptor signaling, we have identified a surface GPR89-family protein that regulates stumpy formation. TbGPR89 is expressed on bloodstream “slender form” trypanosomes, which receive the SIF signal, and when ectopically expressed, TbGPR89 drives stumpy formation in a SIF-pathway-dependent process. Structural modeling of TbGPR89 predicts unexpected similarity to oligopeptide transporters (POT), and when expressed in bacteria, TbGPR89 transports oligopeptides. Conversely, expression of an E. coli POT in trypanosomes drives parasite differentiation, and oligopeptides promote stumpy formation in vitro. Furthermore, the expression of secreted trypanosome oligopeptidases generates a paracrine signal that accelerates stumpy formation in vivo. Peptidase-generated oligopeptide QS signals being received through TbGPR89 provides a mechanism for both trypanosome SIF production and reception. Trypanosomes use quorum sensing to differentiate to transmissible stumpy forms A GPR89 protein with oligopeptide transport activity drives parasite differentiation Oligopeptide mixtures and synthetic di- and tripeptides promote stumpy formation Released parasite oligopeptidases generate the paracrine quorum sensing signal in vivo
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Affiliation(s)
- Federico Rojas
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Eleanor Silvester
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Julie Young
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Rachel Milne
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Mabel Tettey
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Douglas R Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Malcolm D Walkinshaw
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Irene Pérez-Pi
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Manfred Auer
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Helen Denton
- School of Biology, BSRC, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
| | - Terry K Smith
- School of Biology, BSRC, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
| | - Joanne Thompson
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
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11
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Robertson E, Harcus Y, Johnston CJC, Page AP, Walkinshaw MD, Maizels RM, Houston D. DEMONSTRATION OF THE ANTHELMINTIC POTENCY OF MARIMASTAT IN THE HELIGMOSOMOIDES POLYGYRUS RODENT MODEL. J Parasitol 2018; 104:705-709. [PMID: 30085900 DOI: 10.1645/18-33] [Citation(s) in RCA: 1] [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] [Indexed: 12/23/2022] Open
Abstract
In the course of a structure based drug discovery program the known anticancer candidate marimastat was uncovered as a potent inhibitor of an enzyme in nematode cuticle biogenesis. It was shown to kill Caenorhabditis elegans, and the sheep parasites Haemonchus contortus and Teladorsagia circumcinta via an entirely novel nematode-specific pathway, specifically by inhibiting cuticle-remodelling enzymes that the parasites require for the developmentally essential moulting process. This discovery prompted an investigation of the compound's effect on Heligmosomoides polygyrus parasites in a mouse model of helminth infection. Mice were administered the drug via oral gavage daily from day of infection for a period of 2 wk. A second group received the drug via intra-peritoneal implantation of an osmotic minipump for 4 wk. Control groups were administered identical volumes of water by oral gavage in both cases. Counts of H. polygyrus faecal egg and larval load showed that marimastat effected a consistent and significant reduction in egg laying, and a consistent but minor reduction in adult worm load when administered every day, starting on the first day of infection. However, the drug failed to have any significant effect on egg counts or worm burdens when administered to mice with established infections. Therefore, marimastat does not appear to show promise as an anthelmintic in gastrointestinal nematode infections, although other metalloproteases such as batimastat may prove more effective.
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Affiliation(s)
- Elaine Robertson
- * Ashworth Laboratories, Institute of Immunology and Infection, University of Edinburgh, EH9 3FL, U.K
| | - Yvonne Harcus
- † The Queen's Medical Research Institute, 47 Little France Crescent, University of Edinburgh, EH16 4TJ, U.K
| | - Chris J C Johnston
- ‡ Department of Clinical Surgery, Royal Infirmary of Edinburgh, University of Edinburgh, EH16 4SA, U.K
| | - Antony P Page
- § Urquhart Building, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, G61 1QH, U.K
| | - Malcolm D Walkinshaw
- ¶ Michael Swann Building, Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, EH9 3BF, U.K
| | - Rick M Maizels
- ⑊ Sir Graeme Davies Building, Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, G12 8TA, U.K
| | - Douglas Houston
- ** University of Edinburgh School of Biological Sciences Michael Swann Building, Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, EH9 3BF, U.K
- †† 0000-0002-3469-1546
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12
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Gur M, Blackburn EA, Ning J, Narayan V, Ball KL, Walkinshaw MD, Erman B. Molecular dynamics simulations of site point mutations in the TPR domain of cyclophilin 40 identify conformational states with distinct dynamic and enzymatic properties. J Chem Phys 2018; 148:145101. [PMID: 29655319 PMCID: PMC5891347 DOI: 10.1063/1.5019457] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 12/14/2017] [Accepted: 03/13/2018] [Indexed: 02/02/2023] Open
Abstract
Cyclophilin 40 (Cyp40) is a member of the immunophilin family that acts as a peptidyl-prolyl-isomerase enzyme and binds to the heat shock protein 90 (Hsp90). Its structure comprises an N-terminal cyclophilin domain and a C-terminal tetratricopeptide (TPR) domain. Cyp40 is overexpressed in prostate cancer and certain T-cell lymphomas. The groove for Hsp90 binding on the TPR domain includes residues Lys227 and Lys308, referred to as the carboxylate clamp, and is essential for Cyp40-Hsp90 binding. In this study, the effect of two mutations, K227A and K308A, and their combinative mutant was investigated by performing a total of 5.76 μs of all-atom molecular dynamics (MD) simulations in explicit solvent. All simulations, except the K308A mutant, were found to adopt two distinct (extended or compact) conformers defined by different cyclophilin-TPR interdomain distances. The K308A mutant was only observed in the extended form which is observed in the Cyp40 X-ray structure. The wild-type, K227A, and combined mutant also showed bimodal distributions. The experimental melting temperature, Tm, values of the mutants correlate with the degree of compactness with the K308A extended mutant having a marginally lower melting temperature. Another novel measure of compactness determined from the MD data, the "coordination shell volume," also shows a direct correlation with Tm. In addition, the MD simulations show an allosteric effect with the mutations in the remote TPR domain having a pronounced effect on the molecular motions of the enzymatic cyclophilin domain which helps rationalise the experimentally observed increase in enzyme activity measured for all three mutations.
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Affiliation(s)
- Mert Gur
- Department of Mechanical Engineering, Faculty of Mechanical Engineering, Istanbul Technical University (ITU), Suite 445 İnönü Caddesi, No. 65 Gümüşsuyu, 34437 Beyoğlu, Istanbul, Turkey
| | - Elizabeth A Blackburn
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Jia Ning
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Vikram Narayan
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Kathryn L Ball
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Burak Erman
- Department of Chemical and Biological Engineering, Koc University College of Engineering, Eng 146 Rumeli Feneri Yolu, 34450 Sarıyer, Istanbul, Turkey
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13
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Yuan M, Vásquez-Valdivieso MG, McNae IW, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. Structures of Leishmania Fructose-1,6-Bisphosphatase Reveal Species-Specific Differences in the Mechanism of Allosteric Inhibition. J Mol Biol 2017; 429:3075-3089. [PMID: 28882541 PMCID: PMC5639204 DOI: 10.1016/j.jmb.2017.08.010] [Citation(s) in RCA: 9] [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: 07/20/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 11/29/2022]
Abstract
The gluconeogenic enzyme fructose-1,6-bisphosphatase has been proposed as a potential drug target against Leishmania parasites that cause up to 20,000-30,000 deaths annually. A comparison of three crystal structures of Leishmania major fructose-1,6-bisphosphatase (LmFBPase) along with enzyme kinetic data show how AMP acts as an allosteric inhibitor and provides insight into its metal-dependent reaction mechanism. The crystal structure of the apoenzyme form of LmFBPase is a homotetramer in which the dimer of dimers adopts a planar conformation with disordered "dynamic loops". The structure of LmFBPase, complexed with manganese and its catalytic product phosphate, shows the dynamic loops locked into the active sites. A third crystal structure of LmFBPase complexed with its allosteric inhibitor AMP shows an inactive form of the tetramer, in which the dimer pairs are rotated by 18° relative to each other. The three structures suggest an allosteric mechanism in which AMP binding triggers a rearrangement of hydrogen bonds across the large and small interfaces. Retraction of the "effector loop" required for AMP binding releases the side chain of His23 from the dimer-dimer interface. This is coupled with a flip of the side chain of Arg48 which ties down the key catalytic dynamic loop in a disengaged conformation and also locks the tetramer in an inactive rotated T-state. The structure of the effector site of LmFBPase shows different structural features compared with human FBPases, thereby offering a potential and species-specific drug target.
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Affiliation(s)
- Meng Yuan
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Montserrat G Vásquez-Valdivieso
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Iain W McNae
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Paul A M Michels
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Linda A Fothergill-Gilmore
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK.
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14
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Lagger S, Connelly JC, Schweikert G, Webb S, Selfridge J, Ramsahoye BH, Yu M, He C, Sanguinetti G, Sowers LC, Walkinshaw MD, Bird A. MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain. PLoS Genet 2017; 13:e1006793. [PMID: 28498846 PMCID: PMC5446194 DOI: 10.1371/journal.pgen.1006793] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [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: 01/23/2017] [Revised: 05/26/2017] [Accepted: 05/02/2017] [Indexed: 01/10/2023] Open
Abstract
Mutations in the gene encoding the methyl-CG binding protein MeCP2 cause several neurological disorders including Rett syndrome. The di-nucleotide methyl-CG (mCG) is the classical MeCP2 DNA recognition sequence, but additional methylated sequence targets have been reported. Here we show by in vitro and in vivo analyses that MeCP2 binding to non-CG methylated sites in brain is largely confined to the tri-nucleotide sequence mCAC. MeCP2 binding to chromosomal DNA in mouse brain is proportional to mCAC + mCG density and unexpectedly defines large genomic domains within which transcription is sensitive to MeCP2 occupancy. Our results suggest that MeCP2 integrates patterns of mCAC and mCG in the brain to restrain transcription of genes critical for neuronal function. Rett Syndrome is a severe neurological disorder found in approximately 1:10.000 female births. The gene causing most cases of Rett Syndrome has been identified as methyl-CG binding protein 2 (MeCP2) which is an epigenetic reader protein, classically characterized as binding to CpG methylated (mCG) di-nucleotides. Although much research has focused on the binding capacities of MeCP2, its exact mode of action is still controversial. Here we show, that in addition to the classical mCG motif, frequently occurring mCAC tri-nucleotides are also bound by MeCP2. We additionally discover large genomic regions of high mCG + mCAC density that contain neuro-disease relevant genes sensitive to MeCP2 loss or overexpression. Our results re-emphasize MeCP2’s original proposed function as a transcriptional repressor whose purpose is to maintain the delicate balance of neuronal gene expression.
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Affiliation(s)
- Sabine Lagger
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - John C. Connelly
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Gabriele Schweikert
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Shaun Webb
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Jim Selfridge
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Bernard H. Ramsahoye
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Miao Yu
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, United States of America
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, United States of America
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
| | - Guido Sanguinetti
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Lawrence C. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Malcolm D. Walkinshaw
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Adrian Bird
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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15
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Wear MA, Nowicki MW, Blackburn EA, McNae IW, Walkinshaw MD. Thermo-kinetic analysis space expansion for cyclophilin-ligand interactions - identification of a new nonpeptide inhibitor using Biacore™ T200. FEBS Open Bio 2017; 7:533-549. [PMID: 28396838 PMCID: PMC5377415 DOI: 10.1002/2211-5463.12201] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/18/2017] [Accepted: 01/23/2017] [Indexed: 12/31/2022] Open
Abstract
We have established a refined methodology for generating surface plasmon resonance sensor surfaces of recombinant his‐tagged human cyclophilin‐A. Our orientation‐specific stabilisation approach captures his‐tagged protein under ‘physiological conditions’ (150 mm NaCl, pH 7.5) and covalently stabilises it on Ni2+‐nitrilotriacetic acid surfaces, very briefly activated for primary amine‐coupling reactions, producing very stable and active surfaces (≥ 95% specific activity) of cyclophilin‐A. Variation in protein concentration with the same contact time allows straightforward generation of variable density surfaces, with essentially no loss of activity, making the protocol easily adaptable for studying numerous interactions; from very small fragments, ~ 100 Da, to large protein ligands. This new method results in an increased stability and activity of the immobilised protein and allowed us to expand the thermo‐kinetic analysis space, and to determine accurate and robust thermodynamic parameters for the cyclophilin‐A–cyclosporin‐A interaction. Furthermore, the increased sensitivity of the surface allowed identification of a new nonpeptide inhibitor of cyclophilin‐A, from a screen of a fragment library. This fragment, 2,3‐diaminopyridine, bound specifically with a mean affinity of 248 ± 60 μm. The X‐ray structure of this 109‐Da fragment bound in the active site of cyclophilin‐A was solved to a resolution of 1.25 Å (PDB: 5LUD), providing new insight into the molecular details for a potential new series of nonpeptide cyclophilin‐A inhibitors.
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Affiliation(s)
- Martin A Wear
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Matthew W Nowicki
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Elizabeth A Blackburn
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Iain W McNae
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Malcolm D Walkinshaw
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
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16
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France DJ, Stepek G, Houston DR, Williams L, McCormack G, Walkinshaw MD, Page AP. Identification and activity of inhibitors of the essential nematode-specific metalloprotease DPY-31. Bioorg Med Chem Lett 2015; 25:5752-5. [PMID: 26546217 PMCID: PMC4658336 DOI: 10.1016/j.bmcl.2015.10.077] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/23/2015] [Accepted: 10/25/2015] [Indexed: 11/26/2022]
Abstract
Infection by parasitic nematodes is widespread in the developing world causing extensive morbidity and mortality. Furthermore, infection of animals is a global problem, with a substantial impact on food production. Here we identify small molecule inhibitors of a nematode-specific metalloprotease, DPY-31, using both known metalloprotease inhibitors and virtual screening. This strategy successfully identified several μM inhibitors of DPY-31 from both the human filarial nematode Brugia malayi, and the parasitic gastrointestinal nematode of sheep Teladorsagia circumcincta. Further studies using both free living and parasitic nematodes show that these inhibitors elicit the severe body morphology defect 'Dumpy' (Dpy; shorter and fatter), a predominantly non-viable phenotype consistent with mutants lacking the DPY-31 gene. Taken together, these results represent a start point in developing DPY-31 inhibition as a totally novel mechanism for treating infection by parasitic nematodes in humans and animals.
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Affiliation(s)
- David J France
- WestChem School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
| | - Gillian Stepek
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Douglas R Houston
- Institute of Structural & Molecular Biology, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Lewis Williams
- WestChem School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
| | - Gillian McCormack
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Malcolm D Walkinshaw
- Institute of Structural & Molecular Biology, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Antony P Page
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
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17
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Blackburn EA, Wear MA, Landré V, Narayan V, Ning J, Erman B, Ball KL, Walkinshaw MD. Cyclophilin40 isomerase activity is regulated by a temperature-dependent allosteric interaction with Hsp90. Biosci Rep 2015; 35:e00258. [PMID: 26330616 PMCID: PMC4721547 DOI: 10.1042/bsr20150124] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 05/15/2015] [Revised: 06/19/2015] [Accepted: 07/03/2015] [Indexed: 02/06/2023] Open
Abstract
Cyclophilin 40 (Cyp40) comprises an N-terminal cyclophilin domain with peptidyl-prolyl isomerase (PPIase) activity and a C-terminal tetratricopeptide repeat (TPR) domain that binds to the C-terminal-EEVD sequence common to both heat shock protein 70 (Hsp70) and Hsp90. We show in the present study that binding of peptides containing the MEEVD motif reduces the PPIase activity by ∼30%. CD and fluorescence assays show that the TPR domain is less stable than the cyclophilin domain and is stabilized by peptide binding. Isothermal titration calorimetry (ITC) shows that the affinity for the-MEEVD peptide is temperature sensitive in the physiological temperature range. Results from these biophysical studies fit with the MD simulations of the apo and holo (peptide-bound) structures which show a significant reduction in root mean square (RMS) fluctuation in both TPR and cyclophilin domains when-MEEVD is bound. The MD simulations of the apo-protein also highlight strong anti-correlated motions between residues around the PPIase-active site and a band of residues running across four of the seven helices in the TPR domain. Peptide binding leads to a distortion in the shape of the active site and a significant reduction in these strongly anti-correlated motions, providing an explanation for the allosteric effect of ligand binding and loss of PPIase activity. Together the experimental and MD results suggest that on heat shock, dissociation of Cyp40 from complexes mediated by the TPR domain leads to an increased pool of free Cyp40 capable of acting as an isomerase/chaperone in conditions of cellular stress.
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Affiliation(s)
- Elizabeth A Blackburn
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Martin A Wear
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Vivian Landré
- IGMM-Edinburgh Cancer Research Centre, University of Edinburgh, Crewe Road South, EH4 2XR, U.K
| | - Vikram Narayan
- IGMM-Edinburgh Cancer Research Centre, University of Edinburgh, Crewe Road South, EH4 2XR, U.K
| | - Jia Ning
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Burak Erman
- Chemical and Biological Engineering Department, Koc University, Istanbul 34415, Turkey
| | - Kathryn L Ball
- IGMM-Edinburgh Cancer Research Centre, University of Edinburgh, Crewe Road South, EH4 2XR, U.K
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, U.K.
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18
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Narayan V, Landré V, Ning J, Hernychova L, Muller P, Verma C, Walkinshaw MD, Blackburn EA, Ball KL. Protein-Protein Interactions Modulate the Docking-Dependent E3-Ubiquitin Ligase Activity of Carboxy-Terminus of Hsc70-Interacting Protein (CHIP). Mol Cell Proteomics 2015; 14:2973-87. [PMID: 26330542 PMCID: PMC4638040 DOI: 10.1074/mcp.m115.051169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 05/05/2015] [Indexed: 11/07/2022] Open
Abstract
CHIP is a tetratricopeptide repeat (TPR) domain protein that functions as an E3-ubiquitin ligase. As well as linking the molecular chaperones to the ubiquitin proteasome system, CHIP also has a docking-dependent mode where it ubiquitinates native substrates, thereby regulating their steady state levels and/or function. Here we explore the effect of Hsp70 on the docking-dependent E3-ligase activity of CHIP. The TPR-domain is revealed as a binding site for allosteric modulators involved in determining CHIP's dynamic conformation and activity. Biochemical, biophysical and modeling evidence demonstrate that Hsp70-binding to the TPR, or Hsp70-mimetic mutations, regulate CHIP-mediated ubiquitination of p53 and IRF-1 through effects on U-box activity and substrate binding. HDX-MS was used to establish that conformational-inhibition-signals extended from the TPR-domain to the U-box. This underscores inter-domain allosteric regulation of CHIP by the core molecular chaperones. Defining the chaperone-associated TPR-domain of CHIP as a manager of inter-domain communication highlights the potential for scaffolding modules to regulate, as well as assemble, complexes that are fundamental to protein homeostatic control.
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Affiliation(s)
- Vikram Narayan
- From the ‡IGMM, University of Edinburgh Cancer Research Centre, Cell Signalling Unit, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Vivien Landré
- From the ‡IGMM, University of Edinburgh Cancer Research Centre, Cell Signalling Unit, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Jia Ning
- From the ‡IGMM, University of Edinburgh Cancer Research Centre, Cell Signalling Unit, Crewe Road South, Edinburgh EH4 2XR, UK; §CTCB, Institute of Structural and Molecular Biology, University of Edinburgh, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Lenka Hernychova
- ¶Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Petr Muller
- ¶Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Chandra Verma
- ‖Bioinformatics Institute (A*STAR), 30 Biopolis Street, 07-01 Matrix, Singapore 138671; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543; School of Biological Sciences, Nanyang Technological University, 60 Nayang Drive, Singapore 637551
| | - Malcolm D Walkinshaw
- §CTCB, Institute of Structural and Molecular Biology, University of Edinburgh, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Elizabeth A Blackburn
- §CTCB, Institute of Structural and Molecular Biology, University of Edinburgh, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Kathryn L Ball
- From the ‡IGMM, University of Edinburgh Cancer Research Centre, Cell Signalling Unit, Crewe Road South, Edinburgh EH4 2XR, UK;
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19
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Abstract
A comparative molecular dynamics analysis of the pyruvate kinase from Leishmania mexicana is presented in the absence and presence of the allosteric effector fructose 2,6-bisphosphate. Comparisons of the simulations of the large 240 kDa apo and holo tetramers show that binding of fructose 2,6-bisphosphate cools the enzyme and reduces dynamic movement, particularly of the B-domain. The reduced dynamic movement of the holo form traps the pyruvate kinase tetramer in its enzymatically active state with the B-domain acting as a lid to cover the active site. The simulations are also consistent with a transition of the mobile active-site α6' helix, which would adopt a helical conformation in the active R-state and a less structured coil conformation in the inactive T-state. Analysis of the rigid body motions over the trajectory highlights the concerted anticorrelated rigid body rocking motion of the four protomers, which drives the T to R transition. The transitions predicted by these simulations are largely consistent with the Monod-Wyman-Changeux model for allosteric activation but also suggest that rigidification or cooling of the overall structure upon effector binding plays an additional role in enzyme activation.
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Affiliation(s)
- Ankita Naithani
- The Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Taylor
- The Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Burak Erman
- Department of Chemical and Biological Engineering, Koҫ University, Istanbul, Turkey.
| | - Malcolm D Walkinshaw
- The Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
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20
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Healy AR, Houston DR, Remnant L, Huart AS, Brychtova V, Maslon MM, Meers O, Muller P, Krejci A, Blackburn EA, Vojtesek B, Hernychova L, Walkinshaw MD, Westwood NJ, Hupp TR. Discovery of a novel ligand that modulates the protein-protein interactions of the AAA+ superfamily oncoprotein reptin. Chem Sci 2015; 6:3109-3116. [PMID: 28706685 PMCID: PMC5490336 DOI: 10.1039/c4sc03885a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 12/15/2014] [Accepted: 03/20/2015] [Indexed: 12/31/2022] Open
Abstract
Developing approaches to discover protein-protein interactions (PPIs) remains a fundamental challenge. A chemical biology platform is applied here to identify novel PPIs for the AAA+ superfamily oncoprotein reptin. An in silico screen coupled with chemical optimization provided Liddean, a nucleotide-mimetic which modulates reptin's oligomerization status, protein-binding activity and global conformation. Combinatorial peptide phage library screening of Liddean-bound reptin with next generation sequencing identified interaction motifs including a novel reptin docking site on the p53 tumor suppressor protein. Proximity ligation assays demonstrated that endogenous reptin forms a predominantly cytoplasmic complex with its paralog pontin in cancer cells and Liddean promotes a shift of this complex to the nucleus. An emerging view of PPIs in higher eukaryotes is that they occur through a striking diversity of linear peptide motifs. The discovery of a compound that alters reptin's protein interaction landscape potentially leads to novel avenues for therapeutic development.
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Affiliation(s)
- Alan R Healy
- School of Chemistry & Biomedical Sciences Research Complex , University of St Andrews & EaStCHEM , North Haugh, St Andrews , KY16 9ST , UK .
| | - Douglas R Houston
- Centre for Chemical Biology , University of Edinburgh , EH9 3JG , UK .
| | - Lucy Remnant
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
| | - Anne-Sophie Huart
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
| | - Veronika Brychtova
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | - Magda M Maslon
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
| | - Olivia Meers
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
| | - Petr Muller
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | - Adam Krejci
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | | | - Borek Vojtesek
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | - Lenka Hernychova
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | | | - Nicholas J Westwood
- School of Chemistry & Biomedical Sciences Research Complex , University of St Andrews & EaStCHEM , North Haugh, St Andrews , KY16 9ST , UK .
| | - Ted R Hupp
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
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21
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McNeil EM, Astell KR, Ritchie AM, Shave S, Houston DR, Bakrania P, Jones HM, Khurana P, Wallace C, Chapman T, Wear MA, Walkinshaw MD, Saxty B, Melton DW. Inhibition of the ERCC1-XPF structure-specific endonuclease to overcome cancer chemoresistance. DNA Repair (Amst) 2015; 31:19-28. [PMID: 25956741 DOI: 10.1016/j.dnarep.2015.04.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/07/2015] [Accepted: 04/10/2015] [Indexed: 01/23/2023]
Abstract
ERCC1-XPF is a structure-specific endonuclease that is required for the repair of DNA lesions, generated by the widely used platinum-containing cancer chemotherapeutics such as cisplatin, through the Nucleotide Excision Repair and Interstrand Crosslink Repair pathways. Based on mouse xenograft experiments, where ERCC1-deficient melanomas were cured by cisplatin therapy, we proposed that inhibition of ERCC1-XPF could enhance the effectiveness of platinum-based chemotherapy. Here we report the identification and properties of inhibitors against two key targets on ERCC1-XPF. By targeting the ERCC1-XPF interaction domain we proposed that inhibition would disrupt the ERCC1-XPF heterodimer resulting in destabilisation of both proteins. Using in silico screening, we identified an inhibitor that bound to ERCC1-XPF in a biophysical assay, reduced the level of ERCC1-XPF complexes in ovarian cancer cells, inhibited Nucleotide Excision Repair and sensitised melanoma cells to cisplatin. We also utilised high throughput and in silico screening to identify the first reported inhibitors of the other key target, the XPF endonuclease domain. We demonstrate that two of these compounds display specificity in vitro for ERCC1-XPF over two other endonucleases, bind to ERCC1-XPF, inhibit Nucleotide Excision Repair in two independent assays and specifically sensitise Nucleotide Excision Repair-proficient, but not Nucleotide Excision Repair-deficient human and mouse cells to cisplatin.
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Affiliation(s)
- Ewan M McNeil
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Katy R Astell
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Ann-Marie Ritchie
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Steven Shave
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Douglas R Houston
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Preeti Bakrania
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Hayley M Jones
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Puneet Khurana
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Claire Wallace
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Tim Chapman
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Martin A Wear
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Barbara Saxty
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - David W Melton
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
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22
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Shave S, Blackburn EA, Adie J, Houston DR, Auer M, Webster SP, Taylor P, Walkinshaw MD. UFSRAT: Ultra-fast Shape Recognition with Atom Types--the discovery of novel bioactive small molecular scaffolds for FKBP12 and 11βHSD1. PLoS One 2015; 10:e0116570. [PMID: 25659145 PMCID: PMC4319890 DOI: 10.1371/journal.pone.0116570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 07/22/2014] [Accepted: 11/15/2014] [Indexed: 12/31/2022] Open
Abstract
MOTIVATION Using molecular similarity to discover bioactive small molecules with novel chemical scaffolds can be computationally demanding. We describe Ultra-fast Shape Recognition with Atom Types (UFSRAT), an efficient algorithm that considers both the 3D distribution (shape) and electrostatics of atoms to score and retrieve molecules capable of making similar interactions to those of the supplied query. RESULTS Computational optimization and pre-calculation of molecular descriptors enables a query molecule to be run against a database containing 3.8 million molecules and results returned in under 10 seconds on modest hardware. UFSRAT has been used in pipelines to identify bioactive molecules for two clinically relevant drug targets; FK506-Binding Protein 12 and 11β-hydroxysteroid dehydrogenase type 1. In the case of FK506-Binding Protein 12, UFSRAT was used as the first step in a structure-based virtual screening pipeline, yielding many actives, of which the most active shows a KD, app of 281 µM and contains a substructure present in the query compound. Success was also achieved running solely the UFSRAT technique to identify new actives for 11β-hydroxysteroid dehydrogenase type 1, for which the most active displays an IC50 of 67 nM in a cell based assay and contains a substructure radically different to the query. This demonstrates the valuable ability of the UFSRAT algorithm to perform scaffold hops. AVAILABILITY AND IMPLEMENTATION A web-based implementation of the algorithm is freely available at http://opus.bch.ed.ac.uk/ufsrat/.
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Affiliation(s)
- Steven Shave
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Elizabeth A. Blackburn
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Jillian Adie
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Douglas R. Houston
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Manfred Auer
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Scott P. Webster
- University/BHF Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Taylor
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Malcolm D. Walkinshaw
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
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23
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Morgan HP, Zhong W, McNae IW, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. Structures of pyruvate kinases display evolutionarily divergent allosteric strategies. R Soc Open Sci 2014; 1:140120. [PMID: 26064527 PMCID: PMC4448766 DOI: 10.1098/rsos.140120] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/11/2014] [Indexed: 05/13/2023]
Abstract
The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of Trypanosoma cruzi pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the four subunits, coupled with the formation of additional salt bridges across two of the four subunit interfaces. These salt bridges provide increased tetramer stability correlated with an enhanced specificity constant (k cat/S 0.5). A detailed kinetic and structural comparison between the potential drug target PYKs from the pathogenic protists T. cruzi, T. brucei and Leishmania mexicana shows that their allosteric mechanism is conserved. By contrast, a structural comparison of trypanosomatid PYKs with the evolutionarily divergent PYKs of humans and of bacteria shows that they have adopted different allosteric strategies. The underlying principle in each case is to maximize (k cat/S 0.5) by stabilizing and rigidifying the tetramer in an active R-state conformation. However, bacterial and mammalian PYKs have evolved alternative ways of locking the tetramers together. In contrast to the divergent allosteric mechanisms, the PYK active sites are highly conserved across species. Selective disruption of the varied allosteric mechanisms may therefore provide a useful approach for the design of species-specific inhibitors.
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24
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Nicholson J, Scherl A, Way L, Blackburn EA, Walkinshaw MD, Ball KL, Hupp TR. A systems wide mass spectrometric based linear motif screen to identify dominant in-vivo interacting proteins for the ubiquitin ligase MDM2. Cell Signal 2014; 26:1243-57. [PMID: 24583282 DOI: 10.1016/j.cellsig.2014.02.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 02/07/2014] [Accepted: 02/21/2014] [Indexed: 12/24/2022]
Abstract
Linear motifs mediate protein-protein interactions (PPI) that allow expansion of a target protein interactome at a systems level. This study uses a proteomics approach and linear motif sub-stratifications to expand on PPIs of MDM2. MDM2 is a multi-functional protein with over one hundred known binding partners not stratified by hierarchy or function. A new linear motif based on a MDM2 interaction consensus is used to select novel MDM2 interactors based on Nutlin-3 responsiveness in a cell-based proteomics screen. MDM2 binds a subset of peptide motifs corresponding to real proteins with a range of allosteric responses to MDM2 ligands. We validate cyclophilin B as a novel protein with a consensus MDM2 binding motif that is stabilised by Nutlin-3 in vivo, thus identifying one of the few known interactors of MDM2 that is stabilised by Nutlin-3. These data invoke two modes of peptide binding at the MDM2 N-terminus that rely on a consensus core motif to control the equilibrium between MDM2 binding proteins. This approach stratifies MDM2 interacting proteins based on the linear motif feature and provides a new biomarker assay to define clinically relevant Nutlin-3 responsive MDM2 interactors.
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Affiliation(s)
- Judith Nicholson
- Edinburgh Cancer Research Centre, Cell Signalling Unit, University of Edinburgh, EH4 2XR, United Kingdom; Department of Radiation Oncology and Biology, University of Oxford, OX3 7DQ, United Kingdom
| | - Alex Scherl
- Proteomics Core Facility, University of Geneva, Switzerland
| | - Luke Way
- Edinburgh Cancer Research Centre, Cell Signalling Unit, University of Edinburgh, EH4 2XR, United Kingdom
| | - Elizabeth A Blackburn
- Edinburgh Centre for Chemical Biology, University of Edinburgh, EH9 3JG, United Kingdom
| | - Malcolm D Walkinshaw
- Edinburgh Centre for Chemical Biology, University of Edinburgh, EH9 3JG, United Kingdom
| | - Kathryn L Ball
- Edinburgh Cancer Research Centre, Cell Signalling Unit, University of Edinburgh, EH4 2XR, United Kingdom
| | - Ted R Hupp
- Edinburgh Cancer Research Centre, Cell Signalling Unit, University of Edinburgh, EH4 2XR, United Kingdom.
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25
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Brimacombe KR, Walsh MJ, Liu L, Vásquez-Valdivieso MG, Morgan HP, McNae I, Fothergill-Gilmore LA, Michels PAM, Auld DS, Simeonov A, Walkinshaw MD, Shen M, Boxer MB. Identification of ML251, a Potent Inhibitor of T. brucei and T. cruzi Phosphofructokinase. ACS Med Chem Lett 2014; 5:12-7. [PMID: 24900769 DOI: 10.1021/ml400259d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/30/2013] [Indexed: 11/30/2022] Open
Abstract
Human African Trypanosomiasis (HAT) is a severe, often fatal disease caused by the parasitic protist Trypanosoma brucei. The glycolytic pathway has been identified as the sole mechanism for ATP generation in the infective stage of these organisms, and several glycolytic enzymes, phosphofructokinase (PFK) in particular, have shown promise as potential drug targets. Herein, we describe the discovery of ML251, a novel nanomolar inhibitor of T. brucei PFK, and the structure-activity relationships within the series.
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Affiliation(s)
- Kyle R. Brimacombe
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Martin J. Walsh
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Li Liu
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Montserrat G. Vásquez-Valdivieso
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Hugh P. Morgan
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Iain McNae
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Linda A. Fothergill-Gilmore
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Paul A. M. Michels
- Research
Unit for Tropical Diseases, de Duve Institute and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | - Douglas S. Auld
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Malcolm D. Walkinshaw
- Centre
for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings,
Mayfield Road, Edinburgh EH9 3JR, U.K
| | - Min Shen
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew B. Boxer
- National
Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
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26
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Zhong W, Morgan HP, McNae IW, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. `In crystallo' substrate binding triggers major domain movements and reveals magnesium as a co-activator of Trypanosoma brucei pyruvate kinase. Acta Crystallogr D Biol Crystallogr 2013; 69:1768-79. [PMID: 23999300 DOI: 10.1107/s0907444913013875] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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] [Received: 02/07/2013] [Accepted: 05/20/2013] [Indexed: 11/10/2022]
Abstract
The active site of pyruvate kinase (PYK) is located between the AC core of the enzyme and a mobile lid corresponding to domain B. Many PYK structures have already been determined, but the first `effector-only' structure and the first with PEP (the true natural substrate) are now reported for the enzyme from Trypanosoma brucei. PEP soaked into crystals of the enzyme with bound allosteric activator fructose 2,6-bisphosphate (F26BP) and Mg(2+) triggers a substantial 23° rotation of the B domain `in crystallo', resulting in a partially closed active site. The interplay of side chains with Mg(2+) and PEP may explain the mechanism of the domain movement. Furthermore, it is apparent that when F26BP is present but PEP is absent Mg(2+) occupies a position that is distinct from the two canonical Mg(2+)-binding sites at the active site. This third site is adjacent to the active site and involves the same amino-acid side chains as in canonical site 1 but in altered orientations. Site 3 acts to sequester Mg(2+) in a `priming' position such that the enzyme is maintained in its R-state conformation. In this way, Mg(2+) cooperates with F26BP to ensure that the enzyme is in a conformation that has a high affinity for the substrate.
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Affiliation(s)
- Wenhe Zhong
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, Scotland
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27
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Angelopoulos N, Hadjiprocopis A, Walkinshaw MD. Learning Binding Affinity from Augmented High Throughput Screening Data. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch020] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In high throughput screening a large number of molecules are tested against a single target protein to determine binding affinity of each molecule to the target. The objective of such tests within the pharmaceutical industry is to identify potential drug-like lead molecules. Current technology allows for thousands of molecules to be tested inexpensively. The analysis of linking such biological data with molecular properties is thus becoming a major goal in both academic and pharmaceutical research. This chapter details how screening data can be augmented with high-dimensional descriptor data and how machine learning techniques can be utilised to build predictive models. The pyruvate kinase protein is used as a model target throughout the chapter. Binding affinity data from a public repository provide binding information on a large set of screened molecules. The authors consider three machine learning paradigms: Bayesian model averaging, Neural Networks, and Support Vector Machines. The authors apply algorithms from the three paradigms to three subsets of the data and comment on the relative merits of each. They also used the learnt models to classify the molecules in a large in-house molecular database that holds commercially available chemical structures from a large number of suppliers. They discuss the degree of agreement in compounds selected and ranked for three algorithms. Details of the technical challenges in such large scale classification and the ability of each paradigm to cope with these are put forward. The application of machine learning techniques to binding data augmented by high-dimensional can provide a powerful tool in compound testing. The emphasis of this work is on making very few assumptions or technical choices with regard to the machine learning techniques. This is to facilitate application of such techniques by non-experts.
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28
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Abstract
Structure-based virtual screening relies on scoring the predicted binding modes of compounds docked into the target. Because the accuracy of this scoring relies on the accuracy of the docking, methods that increase docking accuracy are valuable. Here, we present a relatively straightforward method for improving the probability of identifying accurately docked poses. The method is similar in concept to consensus scoring schemes, which have been shown to increase ranking power and thus hit rates, but combines information about predicted binding modes rather than predicted binding affinities. The pose prediction success rate of each docking program alone was found in this trial to be 55% for Autodock, 58% for DOCK, and 64% for Vina. By using more than one docking program to predict the binding pose, correct poses were identified in 82% or more of cases, a significant improvement. In a virtual screen, these more reliably posed compounds can be preferentially advanced to subsequent scoring stages to improve hit rates. Consensus docking can be easily introduced into established structure-based virtual screening methodologies.
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Affiliation(s)
- Douglas R Houston
- Institute of Structural and Molecular Biology, University of Edinburgh, Edinburgh, United Kingdom.
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29
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Teo CY, Shave S, Chor ALT, Salleh AB, Rahman MBBA, Walkinshaw MD, Tejo BA. Discovery of a new class of inhibitors for the protein arginine deiminase type 4 (PAD4) by structure-based virtual screening. BMC Bioinformatics 2012; 13 Suppl 17:S4. [PMID: 23282142 PMCID: PMC3521205 DOI: 10.1186/1471-2105-13-s17-s4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [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: 11/10/2022] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is an autoimmune disease with unknown etiology. Anticitrullinated protein autoantibody has been documented as a highly specific autoantibody associated with RA. Protein arginine deiminase type 4 (PAD4) is the enzyme responsible for catalyzing the conversion of peptidylarginine into peptidylcitrulline. PAD4 is a new therapeutic target for RA treatment. In order to search for inhibitors of PAD4, structure-based virtual screening was performed using LIDAEUS (Ligand discovery at Edinburgh university). Potential inhibitors were screened experimentally by inhibition assays. RESULTS Twenty two of the top-ranked water-soluble compounds were selected for inhibitory screening against PAD4. Three compounds showed significant inhibition of PAD4 and their IC50 values were investigated. The structures of the three compounds show no resemblance with previously discovered PAD4 inhibitors, nor with existing drugs for RA treatment. CONCLUSION Three compounds were discovered as potential inhibitors of PAD4 by virtual screening. The compounds are commercially available and can be used as scaffolds to design more potent inhibitors against PAD4.
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Affiliation(s)
- Chian Ying Teo
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Malaysia
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30
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Morgan HP, Walsh MJ, Blackburn EA, Wear MA, Boxer MB, Shen M, Mcnae IW, Nowicki MW, Michels PAM, Auld DS, Fothergill-Gilmore LA, Walkinshaw MD. A new family of covalent inhibitors block nucleotide binding to the active site of pyruvate kinase. Biochem J 2012; 448:67-72. [PMID: 22906073 PMCID: PMC3498827 DOI: 10.1042/bj20121014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [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] [Indexed: 01/22/2023]
Abstract
PYK (pyruvate kinase) plays a central role in the metabolism of many organisms and cell types, but the elucidation of the details of its function in a systems biology context has been hampered by the lack of specific high-affinity small-molecule inhibitors. High-throughput screening has been used to identify a family of saccharin derivatives which inhibit LmPYK (Leishmania mexicana PYK) activity in a time- (and dose-) dependent manner, a characteristic of irreversible inhibition. The crystal structure of DBS {4-[(1,1-dioxo-1,2-benzothiazol-3-yl)sulfanyl]benzoic acid} complexed with LmPYK shows that the saccharin moiety reacts with an active-site lysine residue (Lys335), forming a covalent bond and sterically hindering the binding of ADP/ATP. Mutation of the lysine residue to an arginine residue eliminated the effect of the inhibitor molecule, providing confirmation of the proposed inhibitor mechanism. This lysine residue is conserved in the active sites of the four human PYK isoenzymes, which were also found to be irreversibly inhibited by DBS. X-ray structures of PYK isoforms show structural differences at the DBS-binding pocket, and this covalent inhibitor of PYK provides a chemical scaffold for the design of new families of potentially isoform-specific irreversible inhibitors.
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Affiliation(s)
- Hugh P. Morgan
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Martin J. Walsh
- NIH Chemical Genomics Center, NIH Center for Translational Therapeutics, National Human, Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, U.S.A
| | - Elizabeth A. Blackburn
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Martin A. Wear
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Matthew B. Boxer
- NIH Chemical Genomics Center, NIH Center for Translational Therapeutics, National Human, Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, U.S.A
| | - Min Shen
- NIH Chemical Genomics Center, NIH Center for Translational Therapeutics, National Human, Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, U.S.A
| | - Iain W. Mcnae
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Matthew W. Nowicki
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Paul A. M. Michels
- Research Unit for Tropical Diseases, de Duve Institute and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | - Douglas S. Auld
- NIH Chemical Genomics Center, NIH Center for Translational Therapeutics, National Human, Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, U.S.A
| | - Linda A. Fothergill-Gilmore
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Malcolm D. Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
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Soares DC, Bradshaw NJ, Zou J, Kennaway CK, Hamilton RS, Chen ZA, Wear MA, Blackburn EA, Bramham J, Böttcher B, Millar JK, Barlow PN, Walkinshaw MD, Rappsilber J, Porteous DJ. The mitosis and neurodevelopment proteins NDE1 and NDEL1 form dimers, tetramers, and polymers with a folded back structure in solution. J Biol Chem 2012; 287:32381-93. [PMID: 22843697 PMCID: PMC3463352 DOI: 10.1074/jbc.m112.393439] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [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: 07/04/2012] [Revised: 07/26/2012] [Indexed: 11/06/2022] Open
Abstract
Paralogs NDE1 (nuclear distribution element 1) and NDEL1 (NDE-like 1) are essential for mitosis and neurodevelopment. Both proteins are predicted to have similar structures, based upon high sequence similarity, and they co-complex in mammalian cells. X-ray diffraction studies and homology modeling suggest that their N-terminal regions (residues 8-167) adopt continuous, extended α-helical coiled-coil structures, but no experimentally derived information on the structure of their C-terminal regions or the architecture of the full-length proteins is available. In the case of NDE1, no biophysical data exists. Here we characterize the structural architecture of both full-length proteins utilizing negative stain electron microscopy along with our established paradigm of chemical cross-linking followed by tryptic digestion, mass spectrometry, and database searching, which we enhance using isotope labeling for mixed NDE1-NDEL1. We determined that full-length NDE1 forms needle-like dimers and tetramers in solution, similar to crystal structures of NDEL1, as well as chain-like end-to-end polymers. The C-terminal domain of each protein, required for interaction with key protein partners dynein and DISC1 (disrupted-in-schizophrenia 1), includes a predicted disordered region that allows a bent back structure. This facilitates interaction of the C-terminal region with the N-terminal coiled-coil domain and is in agreement with previous results showing N- and C-terminal regions of NDEL1 and NDE1 cooperating in dynein interaction. It sheds light on recently identified mutations in the NDE1 gene that cause truncation of the encoded protein. Additionally, analysis of mixed NDE1-NDEL1 complexes demonstrates that NDE1 and NDEL1 can interact directly.
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Affiliation(s)
- Dinesh C. Soares
- From the Medical Genetics Section, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Nicholas J. Bradshaw
- From the Medical Genetics Section, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
- the Institut für Neuropathologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Juan Zou
- the Wellcome Trust Centre for Cell Biology and
| | - Christopher K. Kennaway
- the School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Russell S. Hamilton
- the Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | | | - Martin A. Wear
- the Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom, and
| | - Elizabeth A. Blackburn
- the Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom, and
| | - Janice Bramham
- the Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom, and
| | - Bettina Böttcher
- the School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - J. Kirsty Millar
- From the Medical Genetics Section, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Paul N. Barlow
- the Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom, and
| | - Malcolm D. Walkinshaw
- the Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom, and
| | - Juri Rappsilber
- the Wellcome Trust Centre for Cell Biology and
- the Department of Biotechnology, Technische Universität Berlin, 13353 Berlin, Germany
| | - David J. Porteous
- From the Medical Genetics Section, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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Fuad FAA, Fothergill-Gilmore LA, Nowicki MW, Eades LJ, Morgan HP, McNae IW, Michels PAM, Walkinshaw MD. Phosphoglycerate mutase from Trypanosoma brucei is hyperactivated by cobalt in vitro, but not in vivo. Metallomics 2011; 3:1310-7. [PMID: 21993954 DOI: 10.1039/c1mt00119a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Production of ATP by the glycolytic pathway in the mammalian pathogenic stage of protists from the genus Trypanosoma is required for the survival of the parasites. Cofactor-independent phosphoglycerate mutase (iPGAM) is particularly attractive as a drug target because it shows no similarity to the corresponding enzyme in humans, and has also been genetically validated as a target by RNAi experiments. It has previously been shown that trypanosomatid iPGAMs require Co(2+) to reach maximal activity, but the biologically relevant metal has remained unclear. In this paper the metal content in the cytosol of procyclic and bloodstream-form T. brucei (analysed by inductively coupled plasma-optical emission spectroscopy) shows that Mg(2+), Zn(2+) and Fe(2+) were the most abundant, whereas Co(2+) was below the limit of detection (<0.035 μM). The low concentration indicates that Co(2+) is unlikely to be the biologically relevant metal, but that instead, Mg(2+) and/or Zn(2+) may assume this role. Results from metal analysis of purified Leishmania mexicana iPGAM by inductively coupled plasma-mass spectrometry also show high concentrations of Mg(2+) and Zn(2+), and are consistent with this proposal. Our data suggest that in vivo cellular conditions lacking Co(2+) are unable to support the maximal activity of iPGAM, but instead maintain its activity at a relatively low level by using Mg(2+) and/or Zn(2+). The physiological significance of these observations is being pursued by structural, biochemical and biophysical studies.
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Morgan HP, McNae IW, Nowicki MW, Zhong W, Michels PAM, Auld DS, Fothergill-Gilmore LA, Walkinshaw MD. The trypanocidal drug suramin and other trypan blue mimetics are inhibitors of pyruvate kinases and bind to the adenosine site. J Biol Chem 2011; 286:31232-40. [PMID: 21733839 PMCID: PMC3173065 DOI: 10.1074/jbc.m110.212613] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [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: 12/14/2010] [Revised: 06/06/2011] [Indexed: 11/06/2022] Open
Abstract
Ehrlich's pioneering chemotherapeutic experiments published in 1904 (Ehrlich, P., and Shiga, K. (1904) Berlin Klin. Wochenschrift 20, 329-362) described the efficacy of a series of dye molecules including trypan blue and trypan red to eliminate trypanosome infections in mice. The molecular structures of the dyes provided a starting point for the synthesis of suramin, which was developed and used as a trypanocidal drug in 1916 and is still in clinical use. Despite the biological importance of these dye-like molecules, the mode of action on trypanosomes has remained elusive. Here we present crystal structures of suramin and three related dyes in complex with pyruvate kinases from Leishmania mexicana or from Trypanosoma cruzi. The phenyl sulfonate groups of all four molecules (suramin, Ponceau S, acid blue 80, and benzothiazole-2,5-disulfonic acid) bind in the position of ADP/ATP at the active sites of the pyruvate kinases (PYKs). The binding positions in the two different trypanosomatid PYKs are nearly identical. We show that suramin competitively inhibits PYKs from humans (muscle, tumor, and liver isoenzymes, K(i) = 1.1-17 μM), T. cruzi (K(i) = 108 μM), and L. mexicana (K(i) = 116 μM), all of which have similar active sites. Synergistic effects were observed when examining suramin inhibition in the presence of an allosteric effector molecule, whereby IC(50) values decreased up to 2-fold for both trypanosomatid and human PYKs. These kinetic and structural analyses provide insight into the promiscuous inhibition observed for suramin and into the mode of action of the dye-like molecules used in Ehrlich's original experiments.
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Affiliation(s)
- Hugh P. Morgan
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Iain W. McNae
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Matthew W. Nowicki
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Wenhe Zhong
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Paul A. M. Michels
- the Research Unit for Tropical Diseases, de Duve Institute and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium, and
| | - Douglas S. Auld
- the National Institutes of Health Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20850
| | - Linda A. Fothergill-Gilmore
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Malcolm D. Walkinshaw
- From the Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
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Jorda R, Sacerdoti-Sierra N, Voller J, Havlíček L, Kráčalíková K, Nowicki MW, Nasereddin A, Kryštof V, Strnad M, Walkinshaw MD, Jaffe CL. Anti-leishmanial activity of disubstituted purines and related pyrazolo[4,3-d]pyrimidines. Bioorg Med Chem Lett 2011; 21:4233-7. [DOI: 10.1016/j.bmcl.2011.05.076] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/19/2011] [Accepted: 05/20/2011] [Indexed: 12/25/2022]
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Jorda R, Havlíček L, McNae IW, Walkinshaw MD, Voller J, Šturc A, Navrátilová J, Kuzma M, Mistrík M, Bártek J, Strnad M, Kryštof V. Pyrazolo[4,3-d]pyrimidine Bioisostere of Roscovitine: Evaluation of a Novel Selective Inhibitor of Cyclin-Dependent Kinases with Antiproliferative Activity. J Med Chem 2011; 54:2980-93. [DOI: 10.1021/jm200064p] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Radek Jorda
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 78371 Olomouc, Czech Republic
| | - Libor Havlíček
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 78371 Olomouc, Czech Republic
- Isotope Laboratory, Institute of Experimental Botany ASCR, Videnska 1083, 142 20 Prague, Czech Republic
| | - Iain W. McNae
- Structural Biochemistry Group, University of Edinburgh, Michael Swann Building, King’s Buildings, Edinburgh, EH9 3JR, Scotland
| | - Malcolm D. Walkinshaw
- Structural Biochemistry Group, University of Edinburgh, Michael Swann Building, King’s Buildings, Edinburgh, EH9 3JR, Scotland
| | - Jiří Voller
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Department of Growth Regulators, Palacký University, Šlechtitelů 11, Olomouc, CZ-783 71, Czech Republic
| | - Antonín Šturc
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 78371 Olomouc, Czech Republic
| | - Jana Navrátilová
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 78371 Olomouc, Czech Republic
| | - Marek Kuzma
- Laboratory of Molecular Structure Characterization, Institute of Microbiology ASCR, Videnska 1083, 142 20 Prague, Czech Republic
| | - Martin Mistrík
- Laboratory of Genome Integrity and Institute of Molecular and Translational Medicine, Palacký University, Šlechtitelů 11, 78371 Olomouc, Czech Republic
| | - Jiří Bártek
- Laboratory of Genome Integrity and Institute of Molecular and Translational Medicine, Palacký University, Šlechtitelů 11, 78371 Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 78371 Olomouc, Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany ASCR, Šlechtitelů 11, 78371 Olomouc, Czech Republic
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Walker RG, Thomson G, Malone K, Nowicki MW, Brown E, Blake DG, Turner NJ, Walkinshaw MD, Grant KM, Mottram JC. High throughput screens yield small molecule inhibitors of Leishmania CRK3:CYC6 cyclin-dependent kinase. PLoS Negl Trop Dis 2011; 5:e1033. [PMID: 21483720 PMCID: PMC3071374 DOI: 10.1371/journal.pntd.0001033] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [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: 07/13/2010] [Accepted: 03/10/2011] [Indexed: 11/19/2022] Open
Abstract
Background Leishmania species are parasitic protozoa that have a tightly controlled cell cycle, regulated by cyclin-dependent kinases (CDKs). Cdc2-related kinase 3 (CRK3), an essential CDK in Leishmania and functional orthologue of human CDK1, can form an active protein kinase complex with Leishmania cyclins CYCA and CYC6. Here we describe the identification and synthesis of specific small molecule inhibitors of bacterially expressed Leishmania CRK3:CYC6 using a high throughput screening assay and iterative chemistry. We also describe the biological activity of the molecules against Leishmania parasites. Methodology/Principal Findings In order to obtain an active Leishmania CRK3:CYC6 protein kinase complex, we developed a co-expression and co-purification system for Leishmania CRK3 and CYC6 proteins. This active enzyme was used in a high throughput screening (HTS) platform, utilising an IMAP fluorescence polarisation assay. We carried out two chemical library screens and identified specific inhibitors of CRK3:CYC6 that were inactive against the human cyclin-dependent kinase CDK2:CycA. Subsequently, the best inhibitors were tested against 11 other mammalian protein kinases. Twelve of the most potent hits had an azapurine core with structure activity relationship (SAR) analysis identifying the functional groups on the 2 and 9 positions as essential for CRK3:CYC6 inhibition and specificity against CDK2:CycA. Iterative chemistry allowed synthesis of a number of azapurine derivatives with one, compound 17, demonstrating anti-parasitic activity against both promastigote and amastigote forms of L. major. Following the second HTS, 11 compounds with a thiazole core (active towards CRK3:CYC6 and inactive against CDK2:CycA) were tested. Ten of these hits demonstrated anti-parasitic activity against promastigote L. major. Conclusions/Significance The pharmacophores identified from the high throughput screens, and the derivatives synthesised, selectively target the parasite enzyme and represent compounds for future hit-to-lead synthesis programs to develop therapeutics against Leishmania species. Challenges remain in identifying specific CDK inhibitors with both target selectivity and potency against the parasite. CRK3, a cdc2-related serine/threonine protein kinase of the CDK family, is essential for transition through the G2-M phase checkpoint of the Leishmania cell cycle. An expression and purification system has been developed to produce active L. major CRK3 in complex with a cyclin partner, CYC6. CRK3:CYC6 was used to develop an assay suitable for high throughput screening (HTS) using IMAP fluorescence polarization technology. Two compound chemical libraries were screened against CRK3:CYC6 and counter screened against a human cyclin-dependent kinase complex CDK2:CycA. Two main chemical families of inhibitors were identified that specifically inhibited the leishmanial cyclin-dependent kinase, the azapurines and the thiazoles. Structure activity relationship (SAR) analysis of the hits identified the chemical groups attached to the azapurine scaffold that are essential for the inhibition of CRK3:CYC6 protein kinase activity. The CRK3:CYC6 hits were subsequently tested against a panel of 11 mammalian kinases including human CDK1:CYCB, human CDK2:CYCA and human CDK4:CYCD1 to determine their selectivity. Compounds selective to CRK3:CYC6 were tested against Leishmania. Progress towards synthesising potent and selective derivatives of the HTS hits are discussed, with the view to evaluating their potential for the development of novel therapeutics against leishmaniasis.
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Affiliation(s)
- Roderick G. Walker
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Kirk Malone
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Matthew W. Nowicki
- Institute of Structural and Molecular Biology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Elaine Brown
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Nicholas J. Turner
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Malcolm D. Walkinshaw
- Institute of Structural and Molecular Biology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Karen M. Grant
- School of Health & Medicine, Division of Medicine, Lancaster University, Lancaster, United Kingdom
| | - Jeremy C. Mottram
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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Dunsmore CJ, Malone KJ, Bailey KR, Wear MA, Florance H, Shirran S, Barran PE, Page AP, Walkinshaw MD, Turner NJ. Design and synthesis of conformationally constrained cyclophilin inhibitors showing a cyclosporin-A phenotype in C. elegans. Chembiochem 2011; 12:802-10. [PMID: 21337480 DOI: 10.1002/cbic.201000413] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Indexed: 12/23/2022]
Abstract
Cyclophilin A (CypA) is a member of the immunophilin family of proteins and receptor for the immunosuppressant drug cyclosporin A (CsA). Here we describe the design and synthesis of a new class of small-molecule inhibitors for CypA that are based upon a dimedone template. Electrospray mass spectrometry is utilised as an initial screen to quantify the protein affinity of the ligands. Active inhibitors and fluorescently labelled derivatives are then used as chemical probes for investigating the biological role of cyclophilins in the nematode Caenorhabditis elegans.
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Affiliation(s)
- Colin J Dunsmore
- School of Chemistry, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3JJ, UK
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Abstract
The trouble with CDK active-site inhibitors is their tendency to have off-target effects. This is not surprising, as the ATP binding sites of most protein kinases are very similar. Wang et al. (2010) have used some clever screening approaches to identify selective CDK9 inhibitors that drive cancer cells into apoptosis.
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Affiliation(s)
- Matthew W Nowicki
- Centre for Translational and Chemical Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH93JR, Scotland, UK
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Blackburn EA, Maclean JK, Sherborne BS, Walkinshaw MD. Estimating the affinity of protein–ligand complex from changes to the charge-state distribution of a protein in electrospray ionization mass spectrometry. Biochem Biophys Res Commun 2010; 403:190-3. [DOI: 10.1016/j.bbrc.2010.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 11/01/2010] [Indexed: 10/18/2022]
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Fraser JA, Madhumalar A, Blackburn E, Bramham J, Walkinshaw MD, Verma C, Hupp TR. A novel p53 phosphorylation site within the MDM2 ubiquitination signal: II. a model in which phosphorylation at SER269 induces a mutant conformation to p53. J Biol Chem 2010; 285:37773-86. [PMID: 20847049 PMCID: PMC2988382 DOI: 10.1074/jbc.m110.143107] [Citation(s) in RCA: 18] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 09/15/2010] [Indexed: 12/11/2022] Open
Abstract
The p53 DNA-binding domain harbors a conformationally flexible multiprotein binding site that regulates p53 ubiquitination. A novel phosphorylation site exists within this region at Ser(269), whose phosphomimetic mutation inactivates p53. The phosphomimetic p53 (S269D) exhibits characteristics of mutant p53: stable binding to Hsp70 in vivo, elevated ubiquitination in vivo, inactivity in DNA binding and transcription, increased thermoinstability using thermal shift assays, and λ(max) of intrinsic tryptophan fluorescence at 403 nm rather than 346 nm, characteristic of wild type p53. These data indicate that p53 conformational stability is regulated by a phosphoacceptor site within an exposed flexible surface loop and that this can be destabilized by phosphorylation. To test whether other motifs within p53 have similarly evolved, we analyzed the effect of Ser(215) mutation on p53 function because Ser(215) is another inactivating phosphorylation site in the conformationally flexible PAb240 epitope. The p53(S215D) protein is inactive like p53(S269D), whereas p53(S215A) is as active as p53(S269A). However, the double mutant p53(S215A/S269A) was transcriptionally inactive and more thermally unstable than either individual Ser-Ala loop mutant. Molecular dynamics simulations suggest that (i) solvation of phospho-Ser(215) and phospho-Ser(269) by positive charged residues or solvent water leads to local unfolding, which is accompanied by local destabilization of the N-terminal loop and global destabilization of p53, and (ii) the double alanine 215/269 mutation disrupts hydrogen bonding normally stabilized by both Ser(215) and Ser(269). These data indicate that p53 has evolved two serine phosphoacceptor residues within conformationally flexible epitopes that normally stabilize the p53 DNA-binding domain but whose phosphorylation induces a mutant conformation to wild type p53.
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Affiliation(s)
- Jennifer A. Fraser
- From the CRUK p53 Signal Transduction Group, Cell Signaling Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, Scotland, United Kingdom
| | - Arumugam Madhumalar
- the Bioinformatics Institute (A-STAR), 30 Biopolis Street, 07-01 Matrix, Singapore 138671, Singapore
| | - Elizabeth Blackburn
- the Institute of Structural and Molecular Biology, Kings Buildings, Edinburgh EH9 3JR, Scotland, United Kingdom, and
| | - Janice Bramham
- the Institute of Structural and Molecular Biology, Kings Buildings, Edinburgh EH9 3JR, Scotland, United Kingdom, and
| | - Malcolm D. Walkinshaw
- the Institute of Structural and Molecular Biology, Kings Buildings, Edinburgh EH9 3JR, Scotland, United Kingdom, and
| | - Chandra Verma
- the Bioinformatics Institute (A-STAR), 30 Biopolis Street, 07-01 Matrix, Singapore 138671, Singapore
| | - Ted R. Hupp
- From the CRUK p53 Signal Transduction Group, Cell Signaling Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, Scotland, United Kingdom
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Hsin KY, Morgan HP, Shave SR, Hinton AC, Taylor P, Walkinshaw MD. EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities. Nucleic Acids Res 2010; 39:D1042-8. [PMID: 21051336 PMCID: PMC3013767 DOI: 10.1093/nar/gkq878] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [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] [Indexed: 11/25/2022] Open
Abstract
We present the relational database EDULISS (EDinburgh University Ligand Selection System), which stores structural, physicochemical and pharmacophoric properties of small molecules. The database comprises a collection of over 4 million commercially available compounds from 28 different suppliers. A user-friendly web-based interface for EDULISS (available at http://eduliss.bch.ed.ac.uk/) has been established providing a number of data-mining possibilities. For each compound a single 3D conformer is stored along with over 1600 calculated descriptor values (molecular properties). A very efficient method for unique compound recognition, especially for a large scale database, is demonstrated by making use of small subgroups of the descriptors. Many of the shape and distance descriptors are held as pre-calculated bit strings permitting fast and efficient similarity and pharmacophore searches which can be used to identify families of related compounds for biological testing. Two ligand searching applications are given to demonstrate how EDULISS can be used to extract families of molecules with selected structural and biophysical features.
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Affiliation(s)
- Kun-Yi Hsin
- The Centre for Translational and Chemical Biology, The University of Edinburgh, King's Buildings, Edinburgh, UK
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Affiliation(s)
- Marjorie M. Harding
- a Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building , Mayfield Road, Edinburgh , EH9 3JR , UK
| | - Matthew W. Nowicki
- a Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building , Mayfield Road, Edinburgh , EH9 3JR , UK
| | - Malcolm D. Walkinshaw
- a Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building , Mayfield Road, Edinburgh , EH9 3JR , UK
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Brown CJ, Verma CS, Walkinshaw MD, Lane DP. Crystallization of eIF4E complexed with eIF4GI peptide and glycerol reveals distinct structural differences around the cap-binding site. Cell Cycle 2010. [DOI: 10.4161/cc.9.19.13769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Mehio W, Kemp GJ, Taylor P, Walkinshaw MD. Identification of protein binding surfaces using surface triplet propensities. Bioinformatics 2010; 26:2549-55. [DOI: 10.1093/bioinformatics/btq490] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Morgan HP, McNae IW, Hsin KY, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. An improved strategy for the crystallization of Leishmania mexicana pyruvate kinase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:215-8. [PMID: 20208146 DOI: 10.1107/s1744309109053494] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 12/11/2009] [Indexed: 11/10/2022]
Abstract
The inclusion of novel small molecules in crystallization experiments has provided very encouraging results and this method is now emerging as a promising alternative strategy for crystallizing 'problematic' biological macromolecules. These small molecules have the ability to promote lattice formation through stabilizing intermolecular interactions in protein crystals. Here, the use of 1,3,6,8-pyrenetetrasulfonic acid (PTS), which provides a helpful intermolecular bridge between Leishmania mexicana PYK (LmPYK) macromolecules in the crystal, is reported, resulting in the rapid formation of a more stable crystal lattice at neutral pH and greatly improved X-ray diffraction results. The refined structure of the LmPYK-PTS complex revealed the negatively charged PTS molecule to be stacked between positively charged (surface-exposed) arginine side chains from neighbouring LmPYK molecules in the crystal lattice.
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Affiliation(s)
- Hugh P Morgan
- Structural Biochemistry Group, Institute of Structural and Molecular Biology, The University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland
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Morgan HP, McNae IW, Nowicki MW, Hannaert V, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. Allosteric mechanism of pyruvate kinase from Leishmania mexicana uses a rock and lock model. J Biol Chem 2010; 285:12892-8. [PMID: 20123988 DOI: 10.1074/jbc.m109.079905] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Allosteric regulation provides a rate management system for enzymes involved in many cellular processes. Ligand-controlled regulation is easily recognizable, but the underlying molecular mechanisms have remained elusive. We have obtained the first complete series of allosteric structures, in all possible ligated states, for the tetrameric enzyme, pyruvate kinase, from Leishmania mexicana. The transition between inactive T-state and active R-state is accompanied by a simple symmetrical 6 degrees rigid body rocking motion of the A- and C-domain cores in each of the four subunits. However, formation of the R-state in this way is only part of the mechanism; eight essential salt bridge locks that form across the C-C interface provide tetramer rigidity with a coupled 7-fold increase in rate. The results presented here illustrate how conformational changes coupled with effector binding correlate with loss of flexibility and increase in thermal stability providing a general mechanism for allosteric control.
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Affiliation(s)
- Hugh P Morgan
- Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom
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Ludwig C, Wear MA, Walkinshaw MD. Streamlined, automated protocols for the production of milligram quantities of untagged recombinant human cyclophilin-A (hCypA) and untagged human proliferating cell nuclear antigen (hPCNA) using AKTAxpress. Protein Expr Purif 2009; 71:54-61. [PMID: 19995609 PMCID: PMC2837147 DOI: 10.1016/j.pep.2009.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 11/20/2009] [Accepted: 12/03/2009] [Indexed: 12/16/2022]
Abstract
We developed streamlined, automated purification protocols for the production of milligram quantities of untagged recombinant human cyclophilin-A (hCypA) and untagged human proliferating cell nuclear antigen (hPCNA) from Escherichia coli, using the AKTAxpress chromatography system. The automated 2-step (cation exchange and size exclusion) purification protocol for untagged hCypA results in final purity and yields of 93% and approximately 5 mg L(-1) of original cell culture, respectively, in under 12h, including all primary sample processing and column equilibration steps. The novel automated 4-step (anion exchange, desalt, heparin-affinity and size exclusion, in linear sequence) purification protocol for untagged hPCNA results in final purity and yields of 87% and approximately 4 mg L(-1) of original cell culture, respectively, in under 24h, including all primary sample processing and column equilibration steps. This saves in excess of four full working days when compared to the traditional protocol, producing protein with similar final yield, purity and activity. Furthermore, it limits a time-dependent protein aggregation, a problem with the traditional protocol that results in a loss of final yield. Both automated protocols were developed to use generic commercially available pre-packed columns and automatically prepared minimal buffers, designed to eliminate user and system variations, maximize run reproducibility, standardize yield and purity between batches, increase throughput and reduce user input to a minimum. Both protocols represent robust generic methods for the automated production of untagged hCypA and hPCNA.
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Affiliation(s)
- Cornelia Ludwig
- The Edinburgh Protein Production Facility, Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building, Edinburgh EH9 3JR, UK
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Morgan HP, Wear MA, McNae I, Gallagher MP, Walkinshaw MD. Crystallization and X-ray structure of cold-shock protein E from Salmonella typhimurium. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1240-5. [PMID: 20054119 PMCID: PMC2802871 DOI: 10.1107/s1744309109033788] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 08/24/2009] [Indexed: 11/10/2022]
Abstract
In prokaryotic organisms, cold shock triggers the production of a small highly conserved family of cold-shock proteins (CSPs). CSPs have been well studied structurally and functionally in Escherichia coli and Bacillus subtilis, but Salmonella typhimurium CSPs remain relatively uncharacterized. In S. typhimurium, six homologous CSPs have been identified: StCspA-E and StCspH. The crystal structure of cold-shock protein E from S. typhimurium (StCspE) has been determined at 1.1 A resolution and has an R factor of 0.203 after refinement. The three-dimensional structure is similar to those of previously determined CSPs and is composed of five antiparallel beta-strands forming a classic OB fold/five-stranded beta-barrel. This first structure of a CSP from S. typhimurium provides new insight into the cold-shock response of this bacterium.
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Affiliation(s)
- Hugh P. Morgan
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, Scotland
| | - Martin A. Wear
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, Scotland
| | - Iain McNae
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, Scotland
| | - Maurice P. Gallagher
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, Scotland
| | - Malcolm D. Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, Scotland
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Richardson JM, Colloms SD, Finnegan DJ, Walkinshaw MD. Molecular architecture of the Mos1 paired-end complex: the structural basis of DNA transposition in a eukaryote. Cell 2009; 138:1096-108. [PMID: 19766564 DOI: 10.1016/j.cell.2009.07.012] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 04/24/2009] [Accepted: 07/02/2009] [Indexed: 11/26/2022]
Abstract
A key step in cut-and-paste DNA transposition is the pairing of transposon ends before the element is excised and inserted at a new site in its host genome. Crystallographic analyses of the paired-end complex (PEC) formed from precleaved transposon ends and the transposase of the eukaryotic element Mos1 reveals two parallel ends bound to a dimeric enzyme. The complex has a trans arrangement, with each transposon end recognized by the DNA binding region of one transposase monomer and by the active site of the other monomer. Two additional DNA duplexes in the crystal indicate likely binding sites for flanking DNA. Biochemical data provide support for a model of the target capture complex and identify Arg186 to be critical for target binding. Mixing experiments indicate that a transposase dimer initiates first-strand cleavage and suggest a pathway for PEC formation.
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Affiliation(s)
- Julia M Richardson
- School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland.
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Nowicki MW, Kuaprasert B, McNae IW, Morgan HP, Harding MM, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. Crystal structures of Leishmania mexicana phosphoglycerate mutase suggest a one-metal mechanism and a new enzyme subclass. J Mol Biol 2009; 394:535-43. [PMID: 19781556 DOI: 10.1016/j.jmb.2009.09.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 09/11/2009] [Accepted: 09/16/2009] [Indexed: 01/23/2023]
Abstract
The structures of Leishmania mexicana cofactor-independent phosphoglycerate mutase (Lm iPGAM) crystallised with the substrate 3-phosphoglycerate at high and low cobalt concentrations have been solved at 2.00- and 1.90-A resolutions. Both structures are very similar and the active site contains both 3-phosphoglycerate and 2-phosphoglycerate at equal occupancies (50%). Lm iPGAM co-crystallised with the product 2-phosphoglycerate yields the same structure. Two Co(2+) are coordinated within the active site with different geometries and affinities. The cobalt at the M1 site has a distorted octahedral geometry and is present at 100% occupancy. The M2-site Co(2+) binds with distorted tetrahedral geometry, with only partial occupancy, and coordinates with Ser75, the residue involved in phosphotransfer. When the M2 site is occupied, the side chain of Ser75 adopts a position that is unfavourable for catalysis, indicating that this site may not be occupied under physiological conditions and that catalysis may occur via a one-metal mechanism. The geometry of the M2 site suggests that it is possible for Ser75 to be activated for phosphotransfer by H-bonding to nearby residues rather than by metal coordination. The 16 active-site residues of Lm iPGAM are conserved in the Mn-dependent iPGAM from Bacillus stearothermophilus (33% overall sequence identity). However, Lm iPGAM has an inserted tyrosine (Tyr210) that causes the M2 site to diminish in size, consistent with its reduced metal affinity. Tyr210 is present in trypanosomatid and plant iPGAMs, but not in the enzymes from other organisms, indicating that there are two subclasses of iPGAMs.
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Affiliation(s)
- Matthew W Nowicki
- Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, King's Buildings, Edinburgh, UK
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