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Zwirner S, Abu Rmilah AA, Klotz S, Pfaffenroth B, Kloevekorn P, Moschopoulou AA, Schuette S, Haag M, Selig R, Li K, Zhou W, Nelson E, Poso A, Chen H, Amiot B, Jia Y, Minshew A, Michalak G, Cui W, Rist E, Longerich T, Jung B, Felgendreff P, Trompak O, Premsrirut PK, Gries K, Muerdter TE, Heinkele G, Wuestefeld T, Shapiro D, Weissbach M, Koenigsrainer A, Sipos B, Ab E, Zacarias MO, Theisgen S, Gruenheit N, Biskup S, Schwab M, Albrecht W, Laufer S, Nyberg S, Zender L. First-in-class MKK4 inhibitors enhance liver regeneration and prevent liver failure. Cell 2024; 187:1666-1684.e26. [PMID: 38490194 PMCID: PMC11011246 DOI: 10.1016/j.cell.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Diminished hepatocyte regeneration is a key feature of acute and chronic liver diseases and after extended liver resections, resulting in the inability to maintain or restore a sufficient functional liver mass. Therapies to restore hepatocyte regeneration are lacking, making liver transplantation the only curative option for end-stage liver disease. Here, we report on the structure-based development and characterization (nuclear magnetic resonance [NMR] spectroscopy) of first-in-class small molecule inhibitors of the dual-specificity kinase MKK4 (MKK4i). MKK4i increased liver regeneration upon hepatectomy in murine and porcine models, allowed for survival of pigs in a lethal 85% hepatectomy model, and showed antisteatotic and antifibrotic effects in liver disease mouse models. A first-in-human phase I trial (European Union Drug Regulating Authorities Clinical Trials [EudraCT] 2021-000193-28) with the clinical candidate HRX215 was conducted and revealed excellent safety and pharmacokinetics. Clinical trials to probe HRX215 for prevention/treatment of liver failure after extensive oncological liver resections or after transplantation of small grafts are warranted.
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Affiliation(s)
- Stefan Zwirner
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany; HepaRegeniX GmbH, Tübingen 72072, Germany
| | - Anan A Abu Rmilah
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Sabrina Klotz
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Bent Pfaffenroth
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany
| | - Philip Kloevekorn
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany
| | - Athina A Moschopoulou
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Svenja Schuette
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany
| | - Roland Selig
- HepaRegeniX GmbH, Tübingen 72072, Germany; Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany
| | - Kewei Li
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Wei Zhou
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Erek Nelson
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Antti Poso
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany; School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland; iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
| | - Harvey Chen
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Bruce Amiot
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Yao Jia
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Anna Minshew
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Gregory Michalak
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Wei Cui
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Elke Rist
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Thomas Longerich
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | | | - Philipp Felgendreff
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Omelyan Trompak
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | | | - Katharina Gries
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Thomas E Muerdter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany
| | - Georg Heinkele
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany
| | - Torsten Wuestefeld
- Laboratory for In Vivo Genetics & Gene Therapy, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore; School of Biological Sciences, Nanyang Technological University of Singapore, Singapore 637551, Singapore
| | | | | | - Alfred Koenigsrainer
- iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany; German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Department of General-, Visceral, and Transplant Surgery, University Hospital Tübingen, Tübingen 72076, Germany
| | - Bence Sipos
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Eiso Ab
- ZoBio B.V., Leiden 2333 CH, the Netherlands
| | | | | | | | | | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany; iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany; Department of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tübingen, Tübingen 72076, Germany
| | | | - Stefan Laufer
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), Tübingen 72076, Germany.
| | - Scott Nyberg
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA.
| | - Lars Zender
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany; iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany; German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), Tübingen 72076, Germany.
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2
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Jagger AM, Waudby CA, Irving JA, Christodoulou J, Lomas DA. High-resolution ex vivo NMR spectroscopy of human Z α 1-antitrypsin. Nat Commun 2020; 11:6371. [PMID: 33311470 PMCID: PMC7732992 DOI: 10.1038/s41467-020-20147-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/15/2020] [Indexed: 01/18/2023] Open
Abstract
Genetic mutations predispose the serine protease inhibitor α1-antitrypsin to misfolding and polymerisation within hepatocytes, causing liver disease and chronic obstructive pulmonary disease. This misfolding occurs via a transiently populated intermediate state, but our structural understanding of this process is limited by the instability of recombinant α1-antitrypsin variants in solution. Here we apply NMR spectroscopy to patient-derived samples of α1-antitrypsin at natural isotopic abundance to investigate the consequences of disease-causing mutations, and observe widespread chemical shift perturbations for methyl groups in Z AAT (E342K). By comparison with perturbations induced by binding of a small-molecule inhibitor of misfolding we conclude that they arise from rapid exchange between the native conformation and a well-populated intermediate state. The observation that this intermediate is stabilised by inhibitor binding suggests a paradoxical approach to the targeted treatment of protein misfolding disorders, wherein the stabilisation of disease-associated states provides selectivity while inhibiting further transitions along misfolding pathways.
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Affiliation(s)
- Alistair M Jagger
- UCL Respiratory, Rayne Institute, University College London, London, WC1E 6JF, UK
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK
| | - James A Irving
- UCL Respiratory, Rayne Institute, University College London, London, WC1E 6JF, UK.
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
| | - David A Lomas
- UCL Respiratory, Rayne Institute, University College London, London, WC1E 6JF, UK.
- Institute of Structural and Molecular Biology, University College London and School of Crystallography, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
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Makraki E, Carneiro MG, Heyam A, Eiso AB, Siegal G, Hubbard RE. 1H, 13C, 15N backbone and IVL methyl group resonance assignment of the fungal β-glucosidase from Trichoderma reesei. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:265-268. [PMID: 32562251 PMCID: PMC7462900 DOI: 10.1007/s12104-020-09959-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/16/2020] [Indexed: 05/13/2023]
Abstract
β-glucosidases have received considerable attention due to their essential role in bioethanol production from lignocellulosic biomass. β-glucosidase can hydrolyse cellobiose in cellulose degradation and its low activity has been considered as one of the main limiting steps in the process. Large-scale conversions of cellulose therefore require high enzyme concentration which increases the cost. β-glucosidases with improved activity and thermostability are therefore of great commercial interest. The fungus Trichoderma reseei expresses thermostable cellulolytic enzymes which have been widely studied as attractive targets for industrial applications. Genetically modified β-glucosidases from Trichoderma reseei have been recently commercialised. We have developed an approach in which screening of low molecular weight molecules (fragments) identifies compounds that increase enzyme activity and are currently characterizing fragment-based activators of TrBgl2. A structural analysis of the 55 kDa apo form of TrBgl2 revealed a classical (α/β)8-TIM barrel fold. In the present study we present a partial assignment of backbone chemical shifts, along with those of the Ile (I)-Val (V)-Leu (L) methyl groups of TrBgl2. These data will be used to characterize the interaction of TrBgl2 with the small molecule activators.
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Affiliation(s)
- Eleni Makraki
- YSBL, Department of Chemistry, University of York, Heslington, York, UK
| | | | - Alex Heyam
- YSBL, Department of Chemistry, University of York, Heslington, York, UK
| | - A B Eiso
- ZoBio BV, J.H. Oortweg 19, 2333 CH, Leiden, The Netherlands
| | - Gregg Siegal
- ZoBio BV, J.H. Oortweg 19, 2333 CH, Leiden, The Netherlands
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, Netherlands
| | - Roderick E Hubbard
- YSBL, Department of Chemistry, University of York, Heslington, York, UK.
- Vernalis Research, Granta Park, Abington, Cambridge, UK.
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5
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Marcink TC, Koppisetti RK, Fulcher YG, Van Doren SR. Mapping Lipid Bilayer Recognition Sites of Metalloproteinases and Other Prospective Peripheral Membrane Proteins. Methods Mol Biol 2017; 1579:61-86. [PMID: 28299733 DOI: 10.1007/978-1-4939-6863-3_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Peripheral binding of proteins to lipid bilayers is critical not only in intracellular signaling but also in metalloproteinase shedding of signaling proteins from cell surfaces. Assessment of how proteins recognize fluid bilayers peripherally using crystallography or structure-based predictions has been important but incomplete. Assay of dynamic protein-bilayer interactions in solution has become feasible and reliable using paramagnetic NMR and site-directed fluor labeling. Details of preparations and assay protocols for these spectroscopic measurements of bilayer proximity or contact, respectively, are described.
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Affiliation(s)
- Tara C Marcink
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA
| | - Rama K Koppisetti
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA
- Department of Medical Microbiology and Immunology, Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Yan G Fulcher
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA
| | - Steven R Van Doren
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA.
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6
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Sinha K, Sangani SS, Kehr AD, Rule GS, Jen-Jacobson L. Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex. Biochemistry 2016; 55:6115-6132. [PMID: 27786446 PMCID: PMC5402698 DOI: 10.1021/acs.biochem.6b00919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Metal
ion cofactors can alter the energetics and specificity of
sequence specific protein–DNA interactions, but it is unknown
if the underlying effects on structure and dynamics are local or dispersed
throughout the protein–DNA complex. This work uses EcoRV endonuclease
as a model, and catalytically inactive lanthanide ions, which replace
the Mg2+ cofactor. Nuclear magnetic resonance (NMR) titrations
indicate that four Lu3+ or two La3+ cations
bind, and two new crystal structures confirm that Lu3+ binding
is confined to the active sites. NMR spectra show that the metal-free
EcoRV complex with cognate (GATATC) DNA is structurally distinct from
the nonspecific complex, and that metal ion binding sites are not
assembled in the nonspecific complex. NMR chemical shift perturbations
were determined for 1H–15N amide resonances,
for 1H–13C Ile-δ-CH3 resonances, and for stereospecifically assigned Leu-δ-CH3 and Val-γ-CH3 resonances. Many chemical
shifts throughout the cognate complex are unperturbed, so metal binding
does not induce major conformational changes. However, some large
perturbations of amide and side chain methyl resonances occur as far
as 34 Å from the metal ions. Concerted changes in specific residues
imply that local effects of metal binding are propagated via a β-sheet
and an α-helix. Both amide and methyl resonance perturbations
indicate changes in the interface between subunits of the EcoRV homodimer.
Bound metal ions also affect amide hydrogen exchange rates for distant
residues, including a distant subdomain that contacts DNA phosphates
and promotes DNA bending, showing that metal ions in the active sites,
which relieve electrostatic repulsion between protein and DNA, cause
changes in slow dynamics throughout the complex.
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Affiliation(s)
- Kaustubh Sinha
- Department of Biological Sciences, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States.,Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Sahil S Sangani
- Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Andrew D Kehr
- Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Gordon S Rule
- Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Linda Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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7
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Xiao Y, Warner LR, Latham MP, Ahn NG, Pardi A. Structure-Based Assignment of Ile, Leu, and Val Methyl Groups in the Active and Inactive Forms of the Mitogen-Activated Protein Kinase Extracellular Signal-Regulated Kinase 2. Biochemistry 2015; 54:4307-19. [PMID: 26132046 DOI: 10.1021/acs.biochem.5b00506] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Resonance assignments are the first step in most NMR studies of protein structure, function, and dynamics. Standard protein assignment methods employ through-bond backbone experiments on uniformly (13)C/(15)N-labeled proteins. For larger proteins, this through-bond assignment procedure often breaks down due to rapid relaxation and spectral overlap. The challenges involved in studies of larger proteins led to efficient methods for (13)C labeling of side chain methyl groups, which have favorable relaxation properties and high signal-to-noise. These methyls are often still assigned by linking them to the previously assigned backbone, thus limiting the applications for larger proteins. Here, a structure-based procedure is described for assignment of (13)C(1)H3-labeled methyls by comparing distance information obtained from three-dimensional methyl-methyl nuclear Overhauser effect (NOE) spectroscopy with the X-ray structure. The Ile, Leu, or Val (ILV) methyl type is determined by through-bond experiments, and the methyl-methyl NOE data are analyzed in combination with the known structure. A hierarchical approach was employed that maps the largest observed "NOE-methyl cluster" onto the structure. The combination of identification of ILV methyl type with mapping of the NOE-methyl clusters greatly simplifies the assignment process. This method was applied to the inactive and active forms of the 42-kDa ILV (13)C(1)H3-methyl labeled extracellular signal-regulated kinase 2 (ERK2), leading to assignment of 60% of the methyls, including 90% of Ile residues. A series of ILV to Ala mutants were analyzed, which helped confirm the assignments. These assignments were used to probe the local and long-range effects of ligand binding to inactive and active ERK2.
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Affiliation(s)
- Yao Xiao
- †Department of Chemistry and Biochemistry and ‡BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Lisa R Warner
- †Department of Chemistry and Biochemistry and ‡BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Michael P Latham
- †Department of Chemistry and Biochemistry and ‡BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Natalie G Ahn
- †Department of Chemistry and Biochemistry and ‡BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Arthur Pardi
- †Department of Chemistry and Biochemistry and ‡BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, United States
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