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Alcober‐Boquet L, Zang T, Pietsch L, Suess E, Hartmann M, Proschak E, Gross LZF, Sacerdoti M, Zeuzem S, Rogov VV, Leroux AE, Piiper A, Biondi RM. The PB1 and the ZZ domain of the autophagy receptor p62/SQSTM1 regulate the interaction of p62/SQSTM1 with the autophagosome protein LC3B. Protein Sci 2024; 33:e4840. [PMID: 37984441 PMCID: PMC10751729 DOI: 10.1002/pro.4840] [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: 07/03/2023] [Revised: 10/30/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023]
Abstract
Autophagy is a highly conserved cellular process that allows degradation of large macromolecules. p62/SQSTM1 is a key adaptor protein that interacts both with material to be degraded and with LC3 at the autophagosome, enabling degradation of cargos such as protein aggregates, lipid droplets and damaged organelles by selective autophagy. Dysregulation of autophagy contributes to the pathogenesis of many diseases. In this study, we investigated if the interaction of p62/SQSTM1 with LC3B could be regulated. We purified full-length p62/SQSTM1 and established an in vitro assay that measures the interaction with LC3B. We used the assay to determine the role of the different domains of p62/SQSTM1 in the interaction with LC3B. We identified a mechanism of regulation of p62/SQSTM1 where the ZZ and the PB1 domains regulate the exposure of the LIR-sequence to enable or inhibit the interaction with LC3B. A mutation to mimic the phosphorylation of a site on the ZZ domain leads to increased interaction with LC3B. Also, a small compound that binds to the ZZ domain enhances interaction with LC3B. Dysregulation of these mechanisms in p62/SQSTM1 could have implications for diseases where autophagy is affected. In conclusion, our study highlights the regulated nature of p62/SQSTM1 and its ability to modulate the interaction with LC3B through a LIR-sequence Accessibility Mechanism (LAM). Furthermore, our findings suggest the potential for pharmacological modulation of the exposure of LIR, paving the way for future therapeutic strategies.
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Affiliation(s)
- Lucia Alcober‐Boquet
- Goethe University FrankfurtMedical Clinic 1, Biomedical Research Laboratory, University HospitalFrankfurtGermany
| | - Tabea Zang
- Goethe University FrankfurtMedical Clinic 1, Biomedical Research Laboratory, University HospitalFrankfurtGermany
| | - Larissa Pietsch
- Goethe University FrankfurtMedical Clinic 1, Biomedical Research Laboratory, University HospitalFrankfurtGermany
- German Translational Cancer Network (DKTK)FrankfurtGermany
| | - Evelyn Suess
- Goethe University FrankfurtMedical Clinic 1, Biomedical Research Laboratory, University HospitalFrankfurtGermany
| | - Markus Hartmann
- Institut für Pharmazeutische ChemieGoethe‐Universität FrankfurtFrankfurt am MainGermany
| | - Ewgenij Proschak
- Institut für Pharmazeutische ChemieGoethe‐Universität FrankfurtFrankfurt am MainGermany
| | - Lissy Z. F. Gross
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)—CONICET—Partner Institute of the Max Planck SocietyBuenos AiresArgentina
| | - Mariana Sacerdoti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)—CONICET—Partner Institute of the Max Planck SocietyBuenos AiresArgentina
| | - Stefan Zeuzem
- Goethe University FrankfurtMedical Clinic 1, Biomedical Research Laboratory, University HospitalFrankfurtGermany
| | - Vladimir V. Rogov
- Institut für Pharmazeutische ChemieGoethe‐Universität FrankfurtFrankfurt am MainGermany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life SciencesGoethe UniversityFrankfurtGermany
| | - Alejandro E. Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)—CONICET—Partner Institute of the Max Planck SocietyBuenos AiresArgentina
| | - Albrecht Piiper
- Goethe University FrankfurtMedical Clinic 1, Biomedical Research Laboratory, University HospitalFrankfurtGermany
| | - Ricardo M. Biondi
- Goethe University FrankfurtMedical Clinic 1, Biomedical Research Laboratory, University HospitalFrankfurtGermany
- German Translational Cancer Network (DKTK)FrankfurtGermany
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)—CONICET—Partner Institute of the Max Planck SocietyBuenos AiresArgentina
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2
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Leroux AE, Biondi RM. The choreography of protein kinase PDK1 and its diverse substrate dance partners. Biochem J 2023; 480:1503-1532. [PMID: 37792325 DOI: 10.1042/bcj20220396] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/24/2023] [Accepted: 08/31/2023] [Indexed: 10/05/2023]
Abstract
The protein kinase PDK1 phosphorylates at least 24 distinct substrates, all of which belong to the AGC protein kinase group. Some substrates, such as conventional PKCs, undergo phosphorylation by PDK1 during their synthesis and subsequently get activated by DAG and Calcium. On the other hand, other substrates, including members of the Akt/PKB, S6K, SGK, and RSK families, undergo phosphorylation and activation downstream of PI3-kinase signaling. This review presents two accepted molecular mechanisms that determine the precise and timely phosphorylation of different substrates by PDK1. The first mechanism involves the colocalization of PDK1 with Akt/PKB in the presence of PIP3. The second mechanism involves the regulated docking interaction between the hydrophobic motif (HM) of substrates and the PIF-pocket of PDK1. This interaction, in trans, is equivalent to the molecular mechanism that governs the activity of AGC kinases through their HMs intramolecularly. PDK1 has been instrumental in illustrating the bi-directional allosteric communication between the PIF-pocket and the ATP-binding site and the potential of the system for drug discovery. PDK1's interaction with substrates is not solely regulated by the substrates themselves. Recent research indicates that full-length PDK1 can adopt various conformations based on the positioning of the PH domain relative to the catalytic domain. These distinct conformations of full-length PDK1 can influence the interaction and phosphorylation of substrates. Finally, we critically discuss recent findings proposing that PIP3 can directly regulate the activity of PDK1, which contradicts extensive in vitro and in vivo studies conducted over the years.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
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3
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Sacerdoti M, Gross LZF, Riley AM, Zehnder K, Ghode A, Klinke S, Anand GS, Paris K, Winkel A, Herbrand AK, Godage HY, Cozier GE, Süß E, Schulze JO, Pastor-Flores D, Bollini M, Cappellari MV, Svergun D, Gräwert MA, Aramendia PF, Leroux AE, Potter BVL, Camacho CJ, Biondi RM. Modulation of the substrate specificity of the kinase PDK1 by distinct conformations of the full-length protein. Sci Signal 2023; 16:eadd3184. [PMID: 37311034 DOI: 10.1126/scisignal.add3184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 05/19/2023] [Indexed: 06/15/2023]
Abstract
The activation of at least 23 different mammalian kinases requires the phosphorylation of their hydrophobic motifs by the kinase PDK1. A linker connects the phosphoinositide-binding PH domain to the catalytic domain, which contains a docking site for substrates called the PIF pocket. Here, we used a chemical biology approach to show that PDK1 existed in equilibrium between at least three distinct conformations with differing substrate specificities. The inositol polyphosphate derivative HYG8 bound to the PH domain and disrupted PDK1 dimerization by stabilizing a monomeric conformation in which the PH domain associated with the catalytic domain and the PIF pocket was accessible. In the absence of lipids, HYG8 potently inhibited the phosphorylation of Akt (also termed PKB) but did not affect the intrinsic activity of PDK1 or the phosphorylation of SGK, which requires docking to the PIF pocket. In contrast, the small-molecule valsartan bound to the PIF pocket and stabilized a second distinct monomeric conformation. Our study reveals dynamic conformations of full-length PDK1 in which the location of the linker and the PH domain relative to the catalytic domain determines the selective phosphorylation of PDK1 substrates. The study further suggests new approaches for the design of drugs to selectively modulate signaling downstream of PDK1.
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Affiliation(s)
- Mariana Sacerdoti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Lissy Z F Gross
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Andrew M Riley
- Medicinal Chemistry and Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Karin Zehnder
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Abhijeet Ghode
- Biological Sciences, National University of Singapore, Singapore 119077, Singapore
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires C1405BWE, Argentina
| | - Ganesh Srinivasan Anand
- Biological Sciences, National University of Singapore, Singapore 119077, Singapore
- Department of Chemistry, Huck Institutes of the Life Sciences, Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802, USA
| | - Kristina Paris
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Statistics, University of Pittsburgh, WWPH 1821, Pittsburgh, PA 15213, USA
| | - Angelika Winkel
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Amanda K Herbrand
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - H Yasmin Godage
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Gyles E Cozier
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Evelyn Süß
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Jörg O Schulze
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Daniel Pastor-Flores
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
- KBI Biopharma, Technologielaan 8, B-3001 Leuven, Belgium
| | - Mariela Bollini
- Centro de Investigaciones en Bionanociencias 'Elizabeth Jares-Erijman' CIBION, CONICET, Buenos Aires C1425FQD, Argentina
| | - María Victoria Cappellari
- Centro de Investigaciones en Bionanociencias 'Elizabeth Jares-Erijman' CIBION, CONICET, Buenos Aires C1425FQD, Argentina
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, 22607 Hamburg, Germany
| | - Melissa A Gräwert
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, 22607 Hamburg, Germany
| | - Pedro F Aramendia
- Centro de Investigaciones en Bionanociencias 'Elizabeth Jares-Erijman' CIBION, CONICET, Buenos Aires C1425FQD, Argentina
- Departamento de Química Inorgánica, Analítica y Química Física, FCEN, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Barry V L Potter
- Medicinal Chemistry and Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
- DKTK German Cancer Consortium (DKTK), Frankfurt, Germany
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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Gross LZF, Sacerdoti M, Leroux AE, Ghode A, Anand GS, Schulze JO, Graewert MA, Svergun DI, Klinke S, Biondi RM. Chemical biology and structural studies on the mechanism of regulation of phosphoinositide-dependent protein kinase 1 (PDK1). Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321085913] [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: 11/10/2022] Open
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5
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Gross LZF, Sacerdoti M, Piiper A, Zeuzem S, Leroux AE, Biondi RM. ACE2, the Receptor that Enables Infection by SARS-CoV-2: Biochemistry, Structure, Allostery and Evaluation of the Potential Development of ACE2 Modulators. ChemMedChem 2020; 15:1682-1690. [PMID: 32663362 PMCID: PMC7405163 DOI: 10.1002/cmdc.202000368] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/13/2020] [Indexed: 01/07/2023]
Abstract
Angiotensin converting enzyme 2 (ACE2) is the human receptor that interacts with the spike protein of coronaviruses, including the one that produced the 2020 coronavirus pandemic (COVID-19). Thus, ACE2 is a potential target for drugs that disrupt the interaction of human cells with SARS-CoV-2 to abolish infection. There is also interest in drugs that inhibit or activate ACE2, that is, for cardiovascular disorders or colitis. Compounds binding at alternative sites could allosterically affect the interaction with the spike protein. Herein, we review biochemical, chemical biology, and structural information on ACE2, including the recent cryoEM structures of full-length ACE2. We conclude that ACE2 is very dynamic and that allosteric drugs could be developed to target ACE2. At the time of the 2020 pandemic, we suggest that available ACE2 inhibitors or activators in advanced development should be tested for their ability to allosterically displace the interaction between ACE2 and the spike protein.
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Affiliation(s)
- Lissy Z. F. Gross
- Chemical Biology of Regulatory MechanismsIBioBA-CONICET-Partner Institute of the Max Planck SocietyGodoy Cruz 2390Buenos AiresArgentina
| | - Mariana Sacerdoti
- Chemical Biology of Regulatory MechanismsIBioBA-CONICET-Partner Institute of the Max Planck SocietyGodoy Cruz 2390Buenos AiresArgentina
| | - Albrecht Piiper
- Internal Medicine IFrankfurt University HospitalTheodor-Stern-Kai 7Frankfurt am MainGermany
| | - Stefan Zeuzem
- Internal Medicine IFrankfurt University HospitalTheodor-Stern-Kai 7Frankfurt am MainGermany
| | - Alejandro E. Leroux
- Chemical Biology of Regulatory MechanismsIBioBA-CONICET-Partner Institute of the Max Planck SocietyGodoy Cruz 2390Buenos AiresArgentina
| | - Ricardo M. Biondi
- Chemical Biology of Regulatory MechanismsIBioBA-CONICET-Partner Institute of the Max Planck SocietyGodoy Cruz 2390Buenos AiresArgentina
- Internal Medicine IFrankfurt University HospitalTheodor-Stern-Kai 7Frankfurt am MainGermany
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6
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Leroux AE, Biondi RM. Renaissance of Allostery to Disrupt Protein Kinase Interactions. Trends Biochem Sci 2019; 45:27-41. [PMID: 31690482 DOI: 10.1016/j.tibs.2019.09.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022]
Abstract
Protein-protein interactions often regulate the activity of protein kinases by allosterically modulating the conformation of the ATP-binding site. Bidirectional allostery implies that reverse modulation (i.e., from the ATP-binding site to the interaction and regulatory sites) must also be possible. Here, we review both the allosteric regulation of protein kinases and recent work describing how compounds binding at the ATP-binding site can promote or inhibit protein kinase interactions at regulatory sites via the reverse mechanism. Notably, the pharmaceutical industry has been developing compounds that bind to the ATP-binding site of protein kinases and potently disrupt protein-protein interactions between target protein kinases and their regulatory interacting partners. Learning to modulate allosteric processes will facilitate the development of protein-protein interaction modulators.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina; Department of Internal Medicine I, University Hospital, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; DKTK German Cancer Consortium (DKTK), Frankfurt, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Currier RB, Ulrich K, Leroux AE, Dirdjaja N, Deambrosi M, Bonilla M, Ahmed YL, Adrian L, Antelmann H, Jakob U, Comini MA, Krauth-Siegel RL. An essential thioredoxin-type protein of Trypanosoma brucei acts as redox-regulated mitochondrial chaperone. PLoS Pathog 2019; 15:e1008065. [PMID: 31557263 PMCID: PMC6783113 DOI: 10.1371/journal.ppat.1008065] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 10/08/2019] [Accepted: 09/02/2019] [Indexed: 12/22/2022] Open
Abstract
Most known thioredoxin-type proteins (Trx) participate in redox pathways, using two highly conserved cysteine residues to catalyze thiol-disulfide exchange reactions. Here we demonstrate that the so far unexplored Trx2 from African trypanosomes (Trypanosoma brucei) lacks protein disulfide reductase activity but functions as an effective temperature-activated and redox-regulated chaperone. Immunofluorescence microscopy and fractionated cell lysis revealed that Trx2 is located in the mitochondrion of the parasite. RNA-interference and gene knock-out approaches showed that depletion of Trx2 impairs growth of both mammalian bloodstream and insect stage procyclic parasites. Procyclic cells lacking Trx2 stop proliferation under standard culture conditions at 27°C and are unable to survive prolonged exposure to 37°C, indicating that Trx2 plays a vital role that becomes augmented under heat stress. Moreover, we found that Trx2 contributes to the in vivo infectivity of T. brucei. Remarkably, a Trx2 version, in which all five cysteines were replaced by serine residues, complements for the wildtype protein in conditional knock-out cells and confers parasite infectivity in the mouse model. Characterization of the recombinant protein revealed that Trx2 can coordinate an iron sulfur cluster and is highly sensitive towards spontaneous oxidation. Moreover, we discovered that both wildtype and mutant Trx2 protect other proteins against thermal aggregation and preserve their ability to refold upon return to non-stress conditions. Activation of the chaperone function of Trx2 appears to be triggered by temperature-mediated structural changes and inhibited by oxidative disulfide bond formation. Our studies indicate that Trx2 acts as a novel chaperone in the unique single mitochondrion of T. brucei and reveal a new perspective regarding the physiological function of thioredoxin-type proteins in trypanosomes.
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Affiliation(s)
- Rachel B. Currier
- Biochemie-Zentrum der Universität Heidelberg (BZH), Heidelberg, Germany
| | - Kathrin Ulrich
- Biochemie-Zentrum der Universität Heidelberg (BZH), Heidelberg, Germany
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Natalie Dirdjaja
- Biochemie-Zentrum der Universität Heidelberg (BZH), Heidelberg, Germany
| | - Matías Deambrosi
- Group Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Mariana Bonilla
- Group Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | | | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
- Fachgebiet Geobiotechnologie, Technische Universität Berlin, Berlin, Germany
| | - Haike Antelmann
- Institut für Biologie-Mikrobiologie, Freie Universität Berlin, Berlin, Germany
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Marcelo A. Comini
- Group Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
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8
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Abstract
Allostery is a basic principle that enables proteins to process and transmit cellular information. Protein kinases evolved allosteric mechanisms to transduce cellular signals to downstream signalling components or effector molecules. Protein kinases catalyse the transfer of the terminal phosphate from ATP to protein substrates upon specific stimuli. Protein kinases are targets for the development of small molecule inhibitors for the treatment of human diseases. Drug development has focussed on ATP-binding site, while there is increase interest in the development of drugs targeting alternative sites, i.e. allosteric sites. Here, we review the mechanism of regulation of protein kinases, which often involve the allosteric modulation of the ATP-binding site, enhancing or inhibiting activity. We exemplify the molecular mechanism of allostery in protein kinases downstream of PI3-kinase signalling with a focus on phosphoinositide-dependent protein kinase 1 (PDK1), a model kinase where small compounds can allosterically modulate the conformation of the kinase bidirectionally.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Lissy Z F Gross
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Mariana Sacerdoti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina.
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Frankfurt, Germany.
- DKTK German Cancer Consortium (DKTK), Frankfurt, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Giordana L, Sosa MH, Leroux AE, Mendoza EFR, Petray P, Nowicki C. Molecular and functional characterization of two malic enzymes from Leishmania parasites. Mol Biochem Parasitol 2017; 219:67-76. [PMID: 29128656 DOI: 10.1016/j.molbiopara.2017.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/31/2017] [Accepted: 11/02/2017] [Indexed: 10/18/2022]
Abstract
Leishmania parasites cause a broad spectrum of clinical manifestations in humans and the available clinical treatments are far from satisfactory. Since these pathogens require large amounts of NADPH to maintain intracellular redox homeostasis, oxidoreductases that catalyze the production of NADPH are considered as potential drug targets against these diseases. In the sequenced genomes of most Leishmania spp. two putative malic enzymes (MEs) with an identity of about 55% have been identified. In this work, the ME from L. major (LmjF24.0770, Lmj_ME-70) and its less similar homolog from L. mexicana (LmxM.24.0761, Lmex_ME-61) were cloned and functionally characterized. Both MEs specifically catalyzed NADPH production, but only Lmex_ME-61 was activated by l-aspartate. Unlike the allosterically activated human ME, Lmex_ME-61 exhibited typical hyperbolic curves without any sign of cooperativity in the absence of l-aspartate. Moreover, Lmex_ME-61 and Lmj_ME-70 differ from higher eukaryotic homologs in that they display dimeric instead of tetrameric molecular organization. Homology modeling analysis showed that Lmex_ME-61 and Lmj_ME-70 notably differ in their surface charge distribution; this feature encompasses the coenzyme binding pockets as well. However, in both isozymes, the residues directly involved in the coenzyme binding exhibited a good degree of conservation. Besides, only Lmex_ME-61 and its closest homologs were immunodetected in cell-free extracts from L. mexicana, L. amazonensis and L. braziliensis promastigotes. Our findings provide a first glimpse into the biochemical properties of leishmanial MEs and suggest that MEs could be potentially related to the metabolic differences among the species of Leishmania parasites.
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Affiliation(s)
- Lucila Giordana
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica Biológica (IQUIFIB-CONICET), Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Máximo Hernán Sosa
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones Farmacológicas en alianza estratégica con UBA-CONICET (ININFA) Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET -Partner Institute of the Max Planck Society, Buenos Aires C1415FQD, Argentina
| | - Elkin F Rodas Mendoza
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | - Patricia Petray
- Universidad de Buenos Aires, Instituto de Microbiología y Parasitología Médica (IMPaM-CONICET), Paraguay 2155, C1121ABG, Buenos Aires, Argentina
| | - Cristina Nowicki
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica Biológica (IQUIFIB-CONICET), Junín 956, C1113AAD, Buenos Aires, Argentina.
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10
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Leroux AE, Schulze JO, Biondi RM. AGC kinases, mechanisms of regulation and innovative drug development. Semin Cancer Biol 2017; 48:1-17. [PMID: 28591657 DOI: 10.1016/j.semcancer.2017.05.011] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/16/2017] [Accepted: 05/31/2017] [Indexed: 12/22/2022]
Abstract
The group of AGC kinases consists of 63 evolutionarily related serine/threonine protein kinases comprising PDK1, PKB/Akt, SGK, PKC, PRK/PKN, MSK, RSK, S6K, PKA, PKG, DMPK, MRCK, ROCK, NDR, LATS, CRIK, MAST, GRK, Sgk494, and YANK, while two other families, Aurora and PLK, are the most closely related to the group. Eight of these families are physiologically activated downstream of growth factor signalling, while other AGC kinases are downstream effectors of a wide range of signals. The different AGC kinase families share aspects of their mechanisms of inhibition and activation. In the present review, we update the knowledge of the mechanisms of regulation of different AGC kinases. The conformation of the catalytic domain of many AGC kinases is regulated allosterically through the modulation of the conformation of a regulatory site on the small lobe of the kinase domain, the PIF-pocket. The PIF-pocket acts like an ON-OFF switch in AGC kinases with different modes of regulation, i.e. PDK1, PKB/Akt, LATS and Aurora kinases. In this review, we make emphasis on how the knowledge of the molecular mechanisms of regulation can guide the discovery and development of small allosteric modulators. Molecular probes stabilizing the PIF-pocket in the active conformation are activators, while compounds stabilizing the disrupted site are allosteric inhibitors. One challenge for the rational development of allosteric modulators is the lack of complete structural information of the inhibited forms of full-length AGC kinases. On the other hand, we suggest that the available information derived from molecular biology and biochemical studies can already guide screening strategies for the identification of innovative mode of action molecular probes and the development of selective allosteric drugs for the treatment of human diseases.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina.
| | - Jörg O Schulze
- Research Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina; Research Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Leroux AE, Krauth-Siegel RL. Thiol redox biology of trypanosomatids and potential targets for chemotherapy. Mol Biochem Parasitol 2016; 206:67-74. [DOI: 10.1016/j.molbiopara.2015.11.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/09/2015] [Accepted: 11/18/2015] [Indexed: 02/08/2023]
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Achcar F, Fadda A, Haanstra JR, Kerkhoven EJ, Kim DH, Leroux AE, Papamarkou T, Rojas F, Bakker BM, Barrett MP, Clayton C, Girolami M, Krauth-Siegel RL, Matthews KR, Breitling R. The silicon trypanosome: a test case of iterative model extension in systems biology. Adv Microb Physiol 2014; 64:115-43. [PMID: 24797926 DOI: 10.1016/b978-0-12-800143-1.00003-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing African Trypanosomiasis (sleeping sickness in humans and nagana in animals). Due to some of its unique properties, it has emerged as a popular model organism in systems biology. A predictive quantitative model of glycolysis in the bloodstream form of the parasite has been constructed and updated several times. The Silicon Trypanosome is a project that brings together modellers and experimentalists to improve and extend this core model with new pathways and additional levels of regulation. These new extensions and analyses use computational methods that explicitly take different levels of uncertainty into account. During this project, numerous tools and techniques have been developed for this purpose, which can now be used for a wide range of different studies in systems biology.
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Affiliation(s)
- Fiona Achcar
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Abeer Fadda
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Jurgen R Haanstra
- Department of Pediatrics, Centre for Liver Digestive and Metabolic Diseases, and Systems Biology Centre for Energy Metabolism and Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Eduard J Kerkhoven
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; Systems and Synthetic Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Dong-Hyun Kim
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Theodore Papamarkou
- The Department of Statistical Science and The Centre for Computational Statistics and Machine Learning University College London, London, United Kingdom
| | - Federico Rojas
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Barbara M Bakker
- Department of Pediatrics, Centre for Liver Digestive and Metabolic Diseases, and Systems Biology Centre for Energy Metabolism and Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michael P Barrett
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mark Girolami
- The Department of Statistical Science and The Centre for Computational Statistics and Machine Learning University College London, London, United Kingdom
| | | | - Keith R Matthews
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
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Leroux AE, Haanstra JR, Bakker BM, Krauth-Siegel RL. Dissecting the catalytic mechanism of Trypanosoma brucei trypanothione synthetase by kinetic analysis and computational modeling. J Biol Chem 2013; 288:23751-64. [PMID: 23814051 PMCID: PMC3745322 DOI: 10.1074/jbc.m113.483289] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [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] [Indexed: 02/01/2023] Open
Abstract
In pathogenic trypanosomes, trypanothione synthetase (TryS) catalyzes the synthesis of both glutathionylspermidine (Gsp) and trypanothione (bis(glutathionyl)spermidine (T(SH)2)). Here we present a thorough kinetic analysis of Trypanosoma brucei TryS in a newly developed phosphate buffer system at pH 7.0 and 37 °C, mimicking the physiological environment of the enzyme in the cytosol of bloodstream parasites. Under these conditions, TryS displays Km values for GSH, ATP, spermidine, and Gsp of 34, 18, 687, and 32 μm, respectively, as well as Ki values for GSH and T(SH)2 of 1 mm and 360 μm, respectively. As Gsp hydrolysis has a Km value of 5.6 mm, the in vivo amidase activity is probably negligible. To obtain deeper insight in the molecular mechanism of TryS, we have formulated alternative kinetic models, with elementary reaction steps represented by linear kinetic equations. The model parameters were fitted to the extensive matrix of steady-state data obtained for different substrate/product combinations under the in vivo-like conditions. The best model describes the full kinetic profile and is able to predict time course data that were not used for fitting. This system's biology approach to enzyme kinetics led us to conclude that (i) TryS follows a ter-reactant mechanism, (ii) the intermediate Gsp dissociates from the enzyme between the two catalytic steps, and (iii) T(SH)2 inhibits the enzyme by remaining bound at its product site and, as does the inhibitory GSH, by binding to the activated enzyme complex. The newly detected concerted substrate and product inhibition suggests that TryS activity is tightly regulated.
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Affiliation(s)
- Alejandro E Leroux
- Biochemie-Zentrum der Universität Heidelberg, D-69120 Heidelberg, Germany
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Abstract
SIGNIFICANCE Parasitic infections continue to be a major problem for global human health. Vaccines are practically not available and chemotherapy is highly unsatisfactory. One approach toward a novel antiparasitic drug development is to unravel pathways that may be suited as future targets. Parasitic organisms show a remarkable diversity with respect to the nature and functions of their main low-molecular-mass antioxidants and many of them developed pathways that do not have a counterpart in their mammalian hosts. RECENT ADVANCES Work of the last years disclosed the individual antioxidants employed by parasites and their distinct pathways. Entamoeba, Trichomonas, and Giardia directly use cysteine as main low-molecular-mass thiol but have divergent cysteine metabolisms. Malarial parasites rely exclusively on cysteine uptake and generate glutathione (GSH) as main free thiol as do metazoan parasites. Trypanosomes and Leishmania have a unique trypanothione-based thiol metabolism but employ individual mechanisms for their cysteine supply. In addition, some trypanosomatids synthesize ovothiol A and/or ascorbate. Various essential parasite enzymes such as trypanothione synthetase and trypanothione reductase in Trypanosomatids and the Schistosoma thioredoxin GSH reductase are currently intensively explored as drug target molecules. CRITICAL ISSUES Essentiality is a prerequisite but not a sufficient property of an enzyme to become a suited drug target. The availability of an appropriate in vivo screening system and many other factors are equally important. FUTURE DIRECTIONS The current organism-wide RNA-interference and proteome analyses are supposed to reveal many more interesting candidates for future drug development approaches directed against the parasite antioxidant defense systems.
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Leroux AE, Maugeri DA, Cazzulo JJ, Nowicki C. Functional characterization of NADP-dependent isocitrate dehydrogenase isozymes from Trypanosoma cruzi. Mol Biochem Parasitol 2011; 177:61-4. [PMID: 21291916 DOI: 10.1016/j.molbiopara.2011.01.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 01/07/2011] [Accepted: 01/21/2011] [Indexed: 11/18/2022]
Abstract
Trypanosoma cruzi exhibits two putative isocitrate dehydrogenases (IDHs). Both idh genes were cloned and the recombinant enzymes expressed in Escherichia coli. Our results showed that T. cruzi IDHs are strictly dependent on NADP(+) and display apparent affinities towards isocitrate and the coenzyme in the low micromolar range. In T. cruzi, IDHs are cytosolic and mitochondrial enzymes, and there is no evidence for the typical Krebs cycle-related NAD-dependent IDH. Hence, like in Trypanosoma brucei, the Krebs cycle is not a canonical route in T. cruzi. However, the citrate produced in the mitochondrion could be isomerized into isocitrate in the cytosol and the mitochondrion by means of the putative aconitase, which would provide the substrate for both IDHs. The cytosolic IDH is significantly more abundant in amastigotes, cell-derived and metacyclic trypomastigotes than in epimastigotes. This observation fits in well with the expected oxidative burst this pathogen has to face when infecting the mammalian host.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Química y Fisicoquímica Biológica IQUIFIB-CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina.
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Leroux AE, Maugeri DA, Opperdoes FR, Cazzulo JJ, Nowicki C. Comparative studies on the biochemical properties of the malic enzymes from Trypanosoma cruzi and Trypanosoma brucei. FEMS Microbiol Lett 2010; 314:25-33. [PMID: 21105905 DOI: 10.1111/j.1574-6968.2010.02142.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Comparative studies showed that, like Trypanosoma cruzi, Trypanosoma brucei exhibits functional cytosolic and mitochondrial malic enzymes (MEs), which are specifically linked to NADP. Kinetic studies provided evidence that T. cruzi and T. brucei MEs display similarly high affinities towards NADP(+) and are also almost equally efficient in catalyzing the production of NADPH. Nevertheless, in contrast to the cytosolic ME from T. cruzi, which is highly activated by l-aspartate (over 10-fold), the T. brucei homologue is slightly more active (50%) in the presence of this amino acid. In T. brucei, both isozymes appear to be clearly more abundant in the insect stage, although they can be immunodetected in the bloodstream forms. By contrast, in T. cruzi the expression of the mitochondrial ME seems to be clearly upregulated in amastigotes, whereas the cytosolic isoform appears to be more abundant in the insect stages of the parasite. It might be hypothesized that in those environments where glucose is very low or absent, these pathogens depend on NADP-linked dehydrogenases such as the MEs for NADPH production, as in those conditions the pentose phosphate pathway cannot serve as a source of essential reducing power.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Química y Fisicoquímica Biológica IQUIFIB-CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
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