1
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Hunziker D, Reinehr S, Palmhof M, Wagner N, Biniasch T, Stute G, Mattei P, Schmitz P, DiGiorgio P, Hert J, Rudolph MG, Benz J, Stihle M, Gsell B, Müller S, Gasser R, Schonhoven N, Ullmer C, Joachim SC. Synthesis, Characterization, and in vivo Evaluation of a Novel Potent Autotaxin-Inhibitor. Front Pharmacol 2022; 12:699535. [PMID: 35126098 PMCID: PMC8807399 DOI: 10.3389/fphar.2021.699535] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
The autotaxin-lysophosphatidic acid (ATX-LPA) signaling pathway plays a role in a variety of autoimmune diseases, such as rheumatoid arthritis or neurodegeneration. A link to the pathogenesis of glaucoma is suggested by an overactive ATX-LPA axis in aqueous humor samples of glaucoma patients. Analysis of such samples suggests that the ATX-LPA axis contributes to the fibrogenic activity and resistance to aqueous humor outflow through the trabecular meshwork. In order to inhibit or modulate this pathway, we developed a new series of ATX-inhibitors containing novel bicyclic and spirocyclic structural motifs. A potent lead compound (IC50 against ATX: 6 nM) with good in vivo PK, favorable in vitro property, and safety profile was generated. This compound leads to lowered LPA levels in vivo after oral administration. Hence, it was suitable for chronic oral treatment in two rodent models of glaucoma, the experimental autoimmune glaucoma (EAG) and the ischemia/reperfusion models. In the EAG model, rats were immunized with an optic nerve antigen homogenate, while controls received sodium chloride. Retinal ischemia/reperfusion (I/R) was induced by elevating the intraocular pressure (IOP) in one eye to 140 mmHg for 60 min, followed by reperfusion, while the other untreated eye served as control. Retinae and optic nerves were evaluated 28 days after EAG or 7 and 14 days after I/R induction. Oral treatment with the optimized ATX-inhibitor lead to reduced retinal ganglion cell (RGC) loss in both glaucoma models. In the optic nerve, the protective effect of ATX inhibition was less effective compared to the retina and only a trend to a weakened neurofilament distortion was detectable. Taken together, these results provide evidence that the dysregulation of the ATX-LPA axis in the aqueous humor of glaucoma patients, in addition to the postulated outflow impairment, might also contribute to RGC loss. The observation that ATX-inhibitor treatment in both glaucoma models did not result in significant IOP increases or decreases after oral treatment indicates that protection from RGC loss due to inhibition of the ATX-LPA axis is independent of an IOP lowering effect.
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Affiliation(s)
- Daniel Hunziker
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Therapeutic Modalities, Small Molecule Research, Roche Innovation Center Basel, Basel, Switzerland
| | - Sabrina Reinehr
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Marina Palmhof
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Natalie Wagner
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Thomas Biniasch
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Gesa Stute
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Patrizio Mattei
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Therapeutic Modalities, Small Molecule Research, Roche Innovation Center Basel, Basel, Switzerland
| | - Petra Schmitz
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Therapeutic Modalities, Small Molecule Research, Roche Innovation Center Basel, Basel, Switzerland
| | - Patrick DiGiorgio
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Therapeutic Modalities, Small Molecule Research, Roche Innovation Center Basel, Basel, Switzerland
| | - Jérôme Hert
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Therapeutic Modalities, Small Molecule Research, Roche Innovation Center Basel, Basel, Switzerland
| | - Markus G. Rudolph
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Therapeutic Modalities, Small Molecule Research, Roche Innovation Center Basel, Basel, Switzerland
| | - Joerg Benz
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Therapeutic Modalities, Small Molecule Research, Roche Innovation Center Basel, Basel, Switzerland
| | - Martine Stihle
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Therapeutic Modalities, Small Molecule Research, Roche Innovation Center Basel, Basel, Switzerland
| | - Bernard Gsell
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Therapeutic Modalities, Small Molecule Research, Roche Innovation Center Basel, Basel, Switzerland
| | - Stephan Müller
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Therapeutic Modalities, Small Molecule Research, Roche Innovation Center Basel, Basel, Switzerland
| | - Rodolfo Gasser
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Therapeutic Modalities, Small Molecule Research, Roche Innovation Center Basel, Basel, Switzerland
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Nina Schonhoven
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Christoph Ullmer
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Ophthalmology Discovery, Roche Innovation Center Basel, Basel, Switzerland
- *Correspondence: Christoph Ullmer, ; Stephanie C. Joachim,
| | - Stephanie C. Joachim
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Bochum, Germany
- *Correspondence: Christoph Ullmer, ; Stephanie C. Joachim,
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2
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Richter H, Satz AL, Bedoucha M, Buettelmann B, Petersen AC, Harmeier A, Hermosilla R, Hochstrasser R, Burger D, Gsell B, Gasser R, Huber S, Hug MN, Kocer B, Kuhn B, Ritter M, Rudolph MG, Weibel F, Molina-David J, Kim JJ, Santos JV, Stihle M, Georges GJ, Bonfil RD, Fridman R, Uhles S, Moll S, Faul C, Fornoni A, Prunotto M. DNA-Encoded Library-Derived DDR1 Inhibitor Prevents Fibrosis and Renal Function Loss in a Genetic Mouse Model of Alport Syndrome. ACS Chem Biol 2019; 14:37-49. [PMID: 30452219 PMCID: PMC6343110 DOI: 10.1021/acschembio.8b00866] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [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: 02/06/2023]
Abstract
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The
importance of Discoidin Domain Receptor 1 (DDR1) in renal fibrosis
has been shown via gene knockout and use of antisense oligonucleotides;
however, these techniques act via a reduction of DDR1 protein, while
we prove the therapeutic potential of inhibiting DDR1 phosphorylation
with a small molecule. To date, efforts to generate a selective small-molecule
to specifically modulate the activity of DDR1 in an in vivo model have been unsuccessful. We performed parallel DNA encoded
library screens against DDR1 and DDR2, and discovered a chemical series
that is highly selective for DDR1 over DDR2. Structure-guided optimization
efforts yielded the potent DDR1 inhibitor 2.45, which
possesses excellent kinome selectivity (including 64-fold selectivity
over DDR2 in a biochemical assay), a clean in vitro safety profile, and favorable pharmacokinetic and physicochemical
properties. As desired, compound 2.45 modulates DDR1
phosphorylation in vitro as well as prevents collagen-induced
activation of renal epithelial cells expressing DDR1. Compound 2.45 preserves renal function and reduces tissue damage in Col4a3–/– mice (the preclinical
mouse model of Alport syndrome) when employing a therapeutic dosing
regime, indicating the real therapeutic value of selectively inhibiting
DDR1 phosphorylation in vivo. Our results may have
wider significance as Col4a3–/– mice also represent a model for chronic kidney disease, a disease
which affects 10% of the global population.
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Affiliation(s)
- Hans Richter
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Alexander L. Satz
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Marc Bedoucha
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Bernd Buettelmann
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Ann C. Petersen
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Anja Harmeier
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Ricardo Hermosilla
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Remo Hochstrasser
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Dominique Burger
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Bernard Gsell
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Rodolfo Gasser
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Sylwia Huber
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Melanie N. Hug
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Buelent Kocer
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Bernd Kuhn
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Martin Ritter
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Markus G. Rudolph
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Franziska Weibel
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
- Ridgeline Therapeutics GmbH, Basel 4070, Switzerland
| | - Judith Molina-David
- Katz Family Division of Nephrology and Hypertension, University of Miami Miller School of Medicine, Miami, Florida 33136, United States
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami Miller School of Medicine, Miami, Florida 33136, United States
| | - Jin-Ju Kim
- Katz Family Division of Nephrology and Hypertension, University of Miami Miller School of Medicine, Miami, Florida 33136, United States
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami Miller School of Medicine, Miami, Florida 33136, United States
| | - Javier Varona Santos
- Katz Family Division of Nephrology and Hypertension, University of Miami Miller School of Medicine, Miami, Florida 33136, United States
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami Miller School of Medicine, Miami, Florida 33136, United States
| | - Martine Stihle
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Guy J. Georges
- Roche Pharma Research and Early Development, Roche Innovation Center, Munich 82377, Germany
| | - R. Daniel Bonfil
- Department of Pathology, College of Medical Sciences, Nova Southeastern University, Fort Lauderdale, Florida 33328, United States
| | - Rafael Fridman
- Department of Pathology, Wayne State University, Detroit, Michigan 48202, United States
| | - Sabine Uhles
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
| | - Solange Moll
- University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Christian Faul
- University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Alessia Fornoni
- Katz Family Division of Nephrology and Hypertension, University of Miami Miller School of Medicine, Miami, Florida 33136, United States
| | - Marco Prunotto
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel 4070, Switzerland
- Office of Innovation, Immunology, Infectious Diseases & Ophthalmology (I2O), Roche and Genentech Late Stage Development, Basel 4070, Switzerland
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3
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Rufer AC, Kusznir E, Burger D, Stihle M, Ruf A, Rudolph MG. Domain swap in the C-terminal ubiquitin-like domain of human doublecortin. Acta Crystallogr D Struct Biol 2018; 74:450-462. [PMID: 29717716 DOI: 10.1107/s2059798318004813] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/23/2018] [Indexed: 11/10/2022]
Abstract
Doublecortin, a microtubule-associated protein that is only produced during neurogenesis, cooperatively binds to microtubules and stimulates microtubule polymerization and cross-linking by unknown mechanisms. A domain swap is observed in the crystal structure of the C-terminal domain of doublecortin. As determined by analytical ultracentrifugation, an open conformation is also present in solution. At higher concentrations, higher-order oligomers of the domain are formed. The domain swap and additional interfaces observed in the crystal lattice can explain the formation of doublecortin tetramers or multimers, in line with the analytical ultracentrifugation data. Taken together, the domain swap offers a mechanism for the observed cooperative binding of doublecortin to microtubules. Doublecortin-induced cross-linking of microtubules can be explained by the same mechanism. The effect of several mutations leading to lissencephaly and double-cortex syndrome can be traced to the domain swap and the proposed self-association of doublecortin.
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Affiliation(s)
- Arne C Rufer
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Eric Kusznir
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Dominique Burger
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Martine Stihle
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Armin Ruf
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Markus G Rudolph
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
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4
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Kuglstatter A, Stihle M, Neumann C, Müller C, Schaefer W, Klein C, Benz J. Structural differences between glycosylated, disulfide-linked heterodimeric Knob-into-Hole Fc fragment and its homodimeric Knob-Knob and Hole-Hole side products. Protein Eng Des Sel 2017; 30:649-656. [PMID: 28985438 DOI: 10.1093/protein/gzx041] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/17/2017] [Indexed: 11/12/2022] Open
Abstract
An increasing number of bispecific therapeutic antibodies are progressing through clinical development. The Knob-into-Hole (KiH) technology uses complementary mutations in the CH3 region of the antibody Fc fragment to achieve heavy chain heterodimerization. Here we describe the X-ray crystal structures of glycosylated and disulfide-engineered heterodimeric KiH Fc fragment and its homodimeric Knob-Knob and Hole-Hole side products. The heterodimer structure confirms the KiH design principle and supports the hypothesis that glycosylation stabilizes a closed Fc conformation. Both homodimer structures show parallel Fc fragment architectures, in contrast to recently reported crystal structures of the corresponding aglycosylated Fc fragments which in the absence of disulfide mutations show an unexpected antiparallel arrangement. The glycosylated Knob-Knob Fc fragment is destabilized as indicated by variability in the relative orientation of its CH3 domains. The glycosylated Hole-Hole Fc fragment shows an unexpected intermolecular disulfide bond via the introduced Y349C Hole mutation which results in a large CH3 domain shift and a new CH3-CH3 interface. The crystal structures of glycosylated, disulfide-linked KiH Fc fragment and its Knob-Knob and Hole-Hole side products reported here will facilitate further design of highly efficient antibody heterodimerization strategies.
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Affiliation(s)
- A Kuglstatter
- Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse, 4070 Basel, Switzerland
| | - M Stihle
- Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse, 4070 Basel, Switzerland
| | - C Neumann
- Therapeutic Modalities, Roche Innovation Center Zurich, Wagistrasse 18, 8962 Schlieren, Switzerland
| | - C Müller
- Therapeutic Modalities, Roche Innovation Center Zurich, Wagistrasse 18, 8962 Schlieren, Switzerland
| | - W Schaefer
- Therapeutic Modalities, Roche Innovation Center Penzberg, Nonnenwald 2, 82372 Penzberg, Germany
| | - C Klein
- Oncology Disease and Translational Area, Roche Innovation Center Zurich, Wagistrasse 18, 8952 Schlieren, Switzerland
| | - J Benz
- Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse, 4070 Basel, Switzerland
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5
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Klein C, Waldhauer I, Nicolini VG, Freimoser-Grundschober A, Nayak T, Vugts DJ, Dunn C, Bolijn M, Benz J, Stihle M, Lang S, Roemmele M, Hofer T, van Puijenbroek E, Wittig D, Moser S, Ast O, Brünker P, Gorr IH, Neumann S, de Vera Mudry MC, Hinton H, Crameri F, Saro J, Evers S, Gerdes C, Bacac M, van Dongen G, Moessner E, Umaña P. Cergutuzumab amunaleukin (CEA-IL2v), a CEA-targeted IL-2 variant-based immunocytokine for combination cancer immunotherapy: Overcoming limitations of aldesleukin and conventional IL-2-based immunocytokines. Oncoimmunology 2017; 6:e1277306. [PMID: 28405498 PMCID: PMC5384349 DOI: 10.1080/2162402x.2016.1277306] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [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: 10/26/2016] [Revised: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 12/11/2022] Open
Abstract
We developed cergutuzumab amunaleukin (CEA-IL2v, RG7813), a novel monomeric CEA-targeted immunocytokine, that comprises a single IL-2 variant (IL2v) moiety with abolished CD25 binding, fused to the C-terminus of a high affinity, bivalent carcinoembryonic antigen (CEA)-specific antibody devoid of Fc-mediated effector functions. Its molecular design aims to (i) avoid preferential activation of regulatory T-cells vs. immune effector cells by removing CD25 binding; (ii) increase the therapeutic index of IL-2 therapy by (a) preferential retention at the tumor by having a lower dissociation rate from CEA-expressing cancer cells vs. IL-2R-expressing cells, (b) avoiding any FcγR-binding and Fc effector functions and (c) reduced binding to endothelial cells expressing CD25; and (iii) improve the pharmacokinetics, and thus convenience of administration, of IL-2. The crystal structure of the IL2v-IL-2Rβγ complex was determined and CEA-IL2v activity was assessed using human immune effector cells. Tumor targeting was investigated in tumor-bearing mice using 89Zr-labeled CEA-IL2v. Efficacy studies were performed in (a) syngeneic mouse models as monotherapy and combined with anti-PD-L1, and in (b) xenograft mouse models in combination with ADCC-mediating antibodies. CEA-IL2v binds to CEA with pM avidity but not to CD25, and consequently did not preferentially activate Tregs. In vivo, CEA-IL2v demonstrated superior pharmacokinetics and tumor targeting compared with a wild-type IL-2-based CEA immunocytokine (CEA-IL2wt). CEA-IL2v strongly expanded NK and CD8+ T cells, skewing the CD8+:CD4+ ratio toward CD8+ T cells both in the periphery and in the tumor, and mediated single agent efficacy in syngeneic MC38-CEA and PancO2-CEA models. Combination with trastuzumab, cetuximab and imgatuzumab, all of human IgG1 isotype, resulted in superior efficacy compared with the monotherapies alone. Combined with anti-PD-L1, CEA-IL2v mediated superior efficacy over the respective monotherapies, and over the combination with an untargeted control immunocytokine. These preclinical data support the ongoing clinical investigation of the cergutuzumab amunaleukin immunocytokine with abolished CD25 binding for the treatment of CEA-positive solid tumors in combination with PD-L1 checkpoint blockade and ADCC competent antibodies.
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Affiliation(s)
- Christian Klein
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Inja Waldhauer
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Valeria G. Nicolini
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | | | - Tapan Nayak
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Danielle J. Vugts
- Roche Pharma Research & Early Development, Department of Radiology & Nuclear Medicine, VU University Medical Center, Amsterdam, the Netherlands
| | - Claire Dunn
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Marije Bolijn
- Roche Pharma Research & Early Development, Department of Radiology & Nuclear Medicine, VU University Medical Center, Amsterdam, the Netherlands
| | - Jörg Benz
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Martine Stihle
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Sabine Lang
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Michaele Roemmele
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Thomas Hofer
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Erwin van Puijenbroek
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - David Wittig
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Samuel Moser
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Oliver Ast
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Peter Brünker
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Ingo H. Gorr
- Roche Pharma Research & Early Development, Roche Innovation Center Munich, Penzberg, Germany
| | - Sebastian Neumann
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Heather Hinton
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Flavio Crameri
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Jose Saro
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Stefan Evers
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Christian Gerdes
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Marina Bacac
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Guus van Dongen
- Roche Pharma Research & Early Development, Department of Radiology & Nuclear Medicine, VU University Medical Center, Amsterdam, the Netherlands
| | - Ekkehard Moessner
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Pablo Umaña
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
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6
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Burger D, Stihle M, Sharma A, Di Lello P, Benz J, D'Arcy B, Debulpaep M, Fry D, Huber W, Kremer T, Laeremans T, Matile H, Ross A, Rufer AC, Schoch G, Steinmetz MO, Steyaert J, Rudolph MG, Thoma R, Ruf A. Crystal Structures of the Human Doublecortin C- and N-terminal Domains in Complex with Specific Antibodies. J Biol Chem 2016; 291:16292-306. [PMID: 27226599 DOI: 10.1074/jbc.m116.726547] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 03/11/2016] [Indexed: 11/06/2022] Open
Abstract
Doublecortin is a microtubule-associated protein produced during neurogenesis. The protein stabilizes microtubules and stimulates their polymerization, which allows migration of immature neurons to their designated location in the brain. Mutations in the gene that impair doublecortin function and cause severe brain formation disorders are located on a tandem repeat of two doublecortin domains. The molecular mechanism of action of doublecortin is only incompletely understood. Anti-doublecortin antibodies, such as the rabbit polyclonal Abcam 18732, are widely used as neurogenesis markers. Here, we report the generation and characterization of antibodies that bind to single doublecortin domains. The antibodies were used as tools to obtain structures of both domains. Four independent crystal structures of the N-terminal domain reveal several distinct open and closed conformations of the peptide linking N- and C-terminal domains, which can be related to doublecortin function. An NMR assignment and a crystal structure in complex with a camelid antibody fragment show that the doublecortin C-terminal domain adopts the same well defined ubiquitin-like fold as the N-terminal domain, despite its reported aggregation and molten globule-like properties. The antibodies' unique domain specificity also renders them ideal research tools to better understand the role of individual domains in doublecortin function. A single chain camelid antibody fragment specific for the C-terminal doublecortin domain affected microtubule binding, whereas a monoclonal mouse antibody specific for the N-terminal domain did not. Together with steric considerations, this suggests that the microtubule-interacting doublecortin domain observed in cryo-electron micrographs is the C-terminal domain rather than the N-terminal one.
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Affiliation(s)
- Dominique Burger
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Martine Stihle
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Ashwani Sharma
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Paola Di Lello
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, Roche, Nutley, New Jersey 07110
| | - Jörg Benz
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Brigitte D'Arcy
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Maja Debulpaep
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, and the Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - David Fry
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, Roche, Nutley, New Jersey 07110
| | - Walter Huber
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Thomas Kremer
- Roche Pharmaceutical Research and Early Development, NORD Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Toon Laeremans
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, and the Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Hugues Matile
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Alfred Ross
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Arne C Rufer
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Guillaume Schoch
- Roche Pharmaceutical Research and Early Development, NORD Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Michel O Steinmetz
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, and the Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Markus G Rudolph
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Ralf Thoma
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Armin Ruf
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
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7
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Hilpert H, Mauser H, Humm R, Anselm L, Kuehne H, Hartmann G, Gruener S, Banner DW, Benz J, Gsell B, Kuglstatter A, Stihle M, Thoma R, Sanchez RA, Iding H, Wirz B, Haap W. Identification of Potent and Selective Cathepsin S Inhibitors Containing Different Central Cyclic Scaffolds. J Med Chem 2013; 56:9789-801. [DOI: 10.1021/jm401528k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hans Hilpert
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Harald Mauser
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Roland Humm
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Lilli Anselm
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Holger Kuehne
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Guido Hartmann
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Sabine Gruener
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - David W. Banner
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Joerg Benz
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Bernard Gsell
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Andreas Kuglstatter
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Martine Stihle
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Ralf Thoma
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Rubén Alvarez Sanchez
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Hans Iding
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Beat Wirz
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
| | - Wolfgang Haap
- Discovery Chemistry, ‡Cardiovascular and
Metabolic Diseases, §Discovery Technologies, ∥Drug Metabolism
and Pharmacokinetics, ⊥Process Research and Synthesis, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel CH-4070, Switzerland
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8
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Banner DW, Gsell B, Benz J, Bertschinger J, Burger D, Brack S, Cuppuleri S, Debulpaep M, Gast A, Grabulovski D, Hennig M, Hilpert H, Huber W, Kuglstatter A, Kusznir E, Laeremans T, Matile H, Miscenic C, Rufer AC, Schlatter D, Steyaert J, Stihle M, Thoma R, Weber M, Ruf A. Mapping the conformational space accessible to BACE2 using surface mutants and cocrystals with Fab fragments, Fynomers and Xaperones. Acta Crystallogr D Biol Crystallogr 2013; 69:1124-37. [DOI: 10.1107/s0907444913006574] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/07/2013] [Indexed: 01/11/2023]
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9
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Ruf A, Stihle M, Benz J, Schmidt M, Sobek H. Structure of gentlyase, the neutral metalloprotease of Paenibacillus polymyxa. Acta Crystallogr D Biol Crystallogr 2013; 69:24-31. [PMID: 23275160 PMCID: PMC3532130 DOI: 10.1107/s0907444912041169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/01/2012] [Indexed: 11/10/2022]
Abstract
Gentlyase is a bacterial extracellular metalloprotease that is widely applied in cell culture and for tissue dissociation and that belongs to the family of thermolysin-like proteases. The structure of thermolysin has been known since 1972 and that of Bacillus cereus neutral protease since 1992. However, the structure determination of other Bacillus neutral proteases has been hindered by their tendency to cannibalistic autolysis. High calcium conditions that allow the concentration and crystallization of the active Gentlyase metalloprotease without autoproteolysis were identified using thermal fluorescent shift assays. X-ray structures of the protease were solved in the absence and in the presence of the inhibitor phosphoramidon at 1.59 and 1.76 Å resolution, respectively. No domain movement was observed upon inhibitor binding, although such movement is thought to be a general feature of the thermolysin-like protease family. Further analysis of the structure shows that the observed calcium dependency of Gentlyase stability may arise from a partly degenerated calcium site Ca1-2 and a deletion near site Ca3.
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Affiliation(s)
- Armin Ruf
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
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10
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Ruf A, Banner DW, Benz J, Bertschinger J, Burger D, Crisci M, Cuppuleri S, Debulpaep M, Grabulovski D, Gsell B, Huber W, Kusznir E, Laeremans T, Matile H, Pecoraro V, Rufer A, Schlatter D, Steyeart J, Stihle M, Thoma R, Weber M, Wiget A. Fyn, Fab, Xap: evaluation of different protein binders as crystallization aids. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312097267] [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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11
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Ellermann M, Lerner C, Burgy G, Ehler A, Bissantz C, Jakob-Roetne R, Paulini R, Allemann O, Tissot H, Grünstein D, Stihle M, Diederich F, Rudolph MG. Catechol-O-methyltransferase in complex with substituted 3′-deoxyribose bisubstrate inhibitors. Acta Crystallogr D Biol Crystallogr 2012; 68:253-60. [DOI: 10.1107/s0907444912001138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 01/10/2012] [Indexed: 11/10/2022]
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12
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Hardegger LA, Kuhn B, Spinnler B, Anselm L, Ecabert R, Stihle M, Gsell B, Thoma R, Diez J, Benz J, Plancher JM, Hartmann G, Isshiki Y, Morikami K, Shimma N, Haap W, Banner DW, Diederich F. Halogen bonding at the active sites of human cathepsin L and MEK1 kinase: efficient interactions in different environments. ChemMedChem 2011; 6:2048-54. [PMID: 21898833 DOI: 10.1002/cmdc.201100353] [Citation(s) in RCA: 104] [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: 07/19/2011] [Indexed: 01/25/2023]
Abstract
In two series of small-molecule ligands, one inhibiting human cathepsin L (hcatL) and the other MEK1 kinase, biological affinities were found to strongly increase when an aryl ring of the inhibitors is substituted with the larger halogens Cl, Br, and I, but to decrease upon F substitution. X-ray co-crystal structure analyses revealed that the higher halides engage in halogen bonding (XB) with a backbone C=O in the S3 pocket of hcatL and in a back pocket of MEK1. While the S3 pocket is located at the surface of the enzyme, which provides a polar environment, the back pocket in MEK1 is deeply buried in the protein and is of pronounced apolar character. This study analyzes environmental effects on XB in protein-ligand complexes. It is hypothesized that energetic gains by XB are predominantly not due to water replacements but originate from direct interactions between the XB donor (Caryl-X) and the XB acceptor (C=O) in the correct geometry. New X-ray co-crystal structures in the same crystal form (space group P2(1)2(1)2(1)) were obtained for aryl chloride, bromide, and iodide ligands bound to hcatL. These high-resolution structures reveal that the backbone C=O group of Gly61 in most hcatL co-crystal structures maintains water solvation while engaging in XB. An aryl-CF3-substituted ligand of hcatL with an unexpectedly high affinity was found to adopt the same binding geometry as the aryl halides, with the CF3 group pointing to the C=O group of Gly61 in the S3 pocket. In this case, a repulsive F2C-F⋅⋅⋅O=C contact apparently is energetically overcompensated by other favorable protein-ligand contacts established by the CF3 group.
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Affiliation(s)
- Leo A Hardegger
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, HCI, 8093 Zürich, Switzerland
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13
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Kuglstatter A, Mueller F, Kusznir E, Gsell B, Stihle M, Thoma R, Benz J, Aspeslet L, Freitag D, Hennig M. Structural basis for the cyclophilin A binding affinity and immunosuppressive potency of E-ISA247 (voclosporin). Acta Crystallogr D Biol Crystallogr 2011; 67:119-23. [PMID: 21245533 PMCID: PMC3045272 DOI: 10.1107/s0907444910051905] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2010] [Accepted: 12/10/2010] [Indexed: 02/07/2023]
Abstract
X-ray crystal structures of the cyclosporin A analogue E-ISA247 (voclosporin) and its stereoisomer Z-ISA247 bound to cyclophilin A suggest the molecular basis for the differences in their binding affinities and immunosuppressive efficacies. E-ISA247 (voclosporin) is a cyclosporin A analogue that is in late-stage clinical development for the treatment of autoimmune diseases and the prevention of organ graft rejection. The X-ray crystal structures of E-ISA247 and its stereoisomer Z-ISA247 bound to cyclophilin A have been determined and their binding affinities were measured to be 15 and 61 nM, respectively, by fluorescence spectroscopy. The higher affinity of E-ISA247 can be explained by superior van der Waals contacts between its unique side chain and cyclophilin A. Comparison with the known ternary structure including calcineurin suggests that the higher immunosuppressive efficacy of E-ISA247 relative to cyclosporin A could be a consequence of structural changes in calcineurin induced by the modified E-ISA247 side chain.
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Hardegger LA, Kuhn B, Spinnler B, Anselm L, Ecabert R, Stihle M, Gsell B, Thoma R, Diez J, Benz J, Plancher J, Hartmann G, Banner DW, Haap W, Diederich F. Systematic Investigation of Halogen Bonding in Protein–Ligand Interactions. Angew Chem Int Ed Engl 2010; 50:314-8. [PMID: 21184410 DOI: 10.1002/anie.201006781] [Citation(s) in RCA: 391] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Leo A. Hardegger
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang‐Pauli‐Strasse 10, HCI, 8093 Zürich (Switzerland), Fax: (+41) 44‐632‐1109
| | - Bernd Kuhn
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Switzerland), Fax: (+41) 61‐688‐8714
| | - Beat Spinnler
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Switzerland), Fax: (+41) 61‐688‐8714
| | - Lilli Anselm
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Switzerland), Fax: (+41) 61‐688‐8714
| | - Robert Ecabert
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Switzerland), Fax: (+41) 61‐688‐8714
| | - Martine Stihle
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Switzerland), Fax: (+41) 61‐688‐8714
| | - Bernard Gsell
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Switzerland), Fax: (+41) 61‐688‐8714
| | - Ralf Thoma
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Switzerland), Fax: (+41) 61‐688‐8714
| | - Joachim Diez
- Expose GmbH, Grabenstrasse 11, 5313 Klingnau (Switzerland)
| | - Jörg Benz
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Switzerland), Fax: (+41) 61‐688‐8714
| | - Jean‐Marc Plancher
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Switzerland), Fax: (+41) 61‐688‐8714
| | - Guido Hartmann
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Switzerland), Fax: (+41) 61‐688‐8714
| | - David W. Banner
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Switzerland), Fax: (+41) 61‐688‐8714
| | - Wolfgang Haap
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Switzerland), Fax: (+41) 61‐688‐8714
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang‐Pauli‐Strasse 10, HCI, 8093 Zürich (Switzerland), Fax: (+41) 44‐632‐1109
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15
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Hardegger LA, Kuhn B, Spinnler B, Anselm L, Ecabert R, Stihle M, Gsell B, Thoma R, Diez J, Benz J, Plancher J, Hartmann G, Banner DW, Haap W, Diederich F. Systematische Untersuchung von Halogenbrücken in Protein‐Ligand‐ Wechselwirkungen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201006781] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Leo A. Hardegger
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang‐Pauli‐Strasse 10, HCI, 8093 Zürich (Schweiz), Fax: (+41) 44‐632‐1109
| | - Bernd Kuhn
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Schweiz), Fax: (+41) 61‐688‐8714
| | - Beat Spinnler
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Schweiz), Fax: (+41) 61‐688‐8714
| | - Lilli Anselm
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Schweiz), Fax: (+41) 61‐688‐8714
| | - Robert Ecabert
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Schweiz), Fax: (+41) 61‐688‐8714
| | - Martine Stihle
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Schweiz), Fax: (+41) 61‐688‐8714
| | - Bernard Gsell
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Schweiz), Fax: (+41) 61‐688‐8714
| | - Ralf Thoma
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Schweiz), Fax: (+41) 61‐688‐8714
| | - Joachim Diez
- Expose GmbH, Grabenstrasse 11, 5313 Klingnau (Schweiz)
| | - Jörg Benz
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Schweiz), Fax: (+41) 61‐688‐8714
| | - Jean‐Marc Plancher
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Schweiz), Fax: (+41) 61‐688‐8714
| | - Guido Hartmann
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Schweiz), Fax: (+41) 61‐688‐8714
| | - David W. Banner
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Schweiz), Fax: (+41) 61‐688‐8714
| | - Wolfgang Haap
- F. Hoffmann‐La Roche AG, Grenzacherstrasse 124, Bau 92, 4070 Basel (Schweiz), Fax: (+41) 61‐688‐8714
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang‐Pauli‐Strasse 10, HCI, 8093 Zürich (Schweiz), Fax: (+41) 44‐632‐1109
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Pappenberger G, Benz J, Gsell B, Hennig M, Ruf A, Stihle M, Thoma R, Rudolph MG. Structure of the Human Fatty Acid Synthase KS–MAT Didomain as a Framework for Inhibitor Design. J Mol Biol 2010; 397:508-19. [DOI: 10.1016/j.jmb.2010.01.066] [Citation(s) in RCA: 37] [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] [Received: 12/30/2009] [Revised: 01/27/2010] [Accepted: 01/27/2010] [Indexed: 12/21/2022]
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Schoch GA, D'Arcy B, Stihle M, Burger D, Bär D, Benz J, Thoma R, Ruf A. Molecular Switch in the Glucocorticoid Receptor: Active and Passive Antagonist Conformations. J Mol Biol 2010; 395:568-77. [DOI: 10.1016/j.jmb.2009.11.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 11/03/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
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18
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Kuglstatter A, Stahl M, Peters JU, Huber W, Stihle M, Schlatter D, Benz J, Ruf A, Roth D, Enderle T, Hennig M. Tyramine fragment binding to BACE-1. Bioorg Med Chem Lett 2008; 18:1304-7. [DOI: 10.1016/j.bmcl.2008.01.032] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2007] [Revised: 12/20/2007] [Accepted: 01/08/2008] [Indexed: 11/30/2022]
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Schärer K, Morgenthaler M, Paulini R, Obst-Sander U, Banner DW, Schlatter D, Benz J, Stihle M, Diederich F. Quantification of cation-pi interactions in protein-ligand complexes: crystal-structure analysis of Factor Xa bound to a quaternary ammonium ion ligand. Angew Chem Int Ed Engl 2006; 44:4400-4. [PMID: 15952226 DOI: 10.1002/anie.200500883] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kaspar Schärer
- Laboratorium für Organische Chemie, ETH Hönggerberg, HCI, 8093 Zürich, Switzerland
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20
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Rufer AC, Thoma R, Benz J, Stihle M, Gsell B, De Roo E, Banner DW, Mueller F, Chomienne O, Hennig M. The crystal structure of carnitine palmitoyltransferase 2 and implications for diabetes treatment. Structure 2006; 14:713-23. [PMID: 16615913 DOI: 10.1016/j.str.2006.01.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [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: 10/20/2005] [Revised: 12/20/2005] [Accepted: 01/27/2006] [Indexed: 10/24/2022]
Abstract
Carnitine palmitoyltransferases 1 and 2 (CPTs) facilitate the import of long-chain fatty acids into mitochondria. Modulation of the catalytic activity of the CPT system is currently under investigation for the development of novel drugs against diabetes mellitus. We report here the 1.6 A resolution structure of the full-length mitochondrial membrane protein CPT-2. The structure of CPT-2 in complex with the generic CPT inhibitor ST1326 ([R]-N-[tetradecylcarbamoyl]-aminocarnitine), a substrate analog mimicking palmitoylcarnitine and currently in clinical trials for diabetes mellitus treatment, was solved at 2.5 A resolution. These structures of CPT-2 provide insight into the function of residues involved in substrate binding and determination of substrate specificity, thereby facilitating the rational design of antidiabetic drugs. We identify a sequence insertion found in CPT-2 that mediates membrane localization. Mapping of mutations described for CPT-2 deficiency, a hereditary disorder of lipid metabolism, implies effects on substrate recognition and structural integrity of CPT-2.
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Affiliation(s)
- Arne C Rufer
- F. Hoffmann-La Roche AG, Pharma Research Discovery, 4070 Basel, Switzerland
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21
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Burgermeister E, Schnoebelen A, Flament A, Benz J, Stihle M, Gsell B, Rufer A, Ruf A, Kuhn B, Märki HP, Mizrahi J, Sebokova E, Niesor E, Meyer M. A novel partial agonist of peroxisome proliferator-activated receptor-gamma (PPARgamma) recruits PPARgamma-coactivator-1alpha, prevents triglyceride accumulation, and potentiates insulin signaling in vitro. Mol Endocrinol 2005; 20:809-30. [PMID: 16373399 DOI: 10.1210/me.2005-0171] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Partial agonists of peroxisome proliferator-activated receptor-gamma (PPARgamma), also termed selective PPARgamma modulators, are expected to uncouple insulin sensitization from triglyceride (TG) storage in patients with type 2 diabetes mellitus. These agents shall thus avoid adverse effects, such as body weight gain, exerted by full agonists such as thiazolidinediones. In this context, we describe the identification and characterization of the isoquinoline derivative PA-082, a prototype of a novel class of non-thiazolidinedione partial PPARgamma ligands. In a cocrystal with PPARgamma it was bound within the ligand-binding pocket without direct contact to helix 12. The compound displayed partial agonism in biochemical and cell-based transactivation assays and caused preferential recruitment of PPARgamma-coactivator-1alpha (PGC1alpha) to the receptor, a feature shared with other selective PPARgamma modulators. It antagonized rosiglitazone-driven transactivation and TG accumulation during de novo adipogenic differentiation of murine C3H10T1/2 mesenchymal stem cells. The latter effect was mimicked by overexpression of wild-type PGC1alpha but not its LXXLL-deficient mutant. Despite failing to promote TG loading, PA-082 induced mRNAs of genes encoding components of insulin signaling and adipogenic differentiation pathways. It potentiated glucose uptake and inhibited the negative cross-talk of TNFalpha on protein kinase B (AKT) phosphorylation in mature adipocytes and HepG2 human hepatoma cells. PGC1alpha is a key regulator of energy expenditure and down-regulated in diabetics. We thus propose that selective recruitment of PGC1alpha to favorable PPARgamma-target genes provides a possible molecular mechanism whereby partial PPARgamma agonists dissociate TG accumulation from insulin signaling.
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Affiliation(s)
- Elke Burgermeister
- Pharmaceuticals Division, Department of Vascular and Metabolic Diseases, Fa. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
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22
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Ruf A, Thoma R, D'Arcy B, Müller F, Kusznir E, Stihle M, Morand O. Crystal structure of oxido squalene cyclase. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305089452] [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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23
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Schlatter D, Thoma R, Küng E, Stihle M, Müller F, Borroni E, Cesura A, Hennig M. Crystal engineering yields crystals of cyclophilin D diffracting to 1.7 A resolution. Acta Crystallogr D Biol Crystallogr 2005; 61:513-9. [PMID: 15858260 DOI: 10.1107/s0907444905003070] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2004] [Accepted: 01/27/2005] [Indexed: 11/10/2022]
Abstract
In the pharmaceutical industry, knowledge of the three-dimensional structure of a specific target facilitates the drug-discovery process. Despite possessing favoured analytical properties such as high purity and monodispersion in light scattering, some proteins are not capable of forming crystals suitable for X-ray analysis. Cyclophilin D, an isoform of cyclophilin that is expressed in the mitochondria, was selected as a drug target for the treatment of cardiac disorders. As the wild-type enzyme defied all attempts at crystallization, protein engineering on the enzyme surface was performed. The K133I mutant gave crystals that diffracted to 1.7 A resolution using in-house X-ray facilities and were suitable for soaking experiments. The crystals were very robust and diffraction was maintained after soaking in 25% DMSO solution: excellent conditions for the rapid analysis of complex structures including crystallographic fragment screening.
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Affiliation(s)
- Daniel Schlatter
- F. Hoffmann-La Roche Ltd, Pharmaceutical Research Discovery, CH-4070 Basel, Switzerland.
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24
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Thoma R, Schulz-Gasch T, D'Arcy B, Benz J, Aebi J, Dehmlow H, Hennig M, Stihle M, Ruf A. Insight into steroid scaffold formation from the structure of human oxidosqualene cyclase. Nature 2004; 432:118-22. [PMID: 15525992 DOI: 10.1038/nature02993] [Citation(s) in RCA: 260] [Impact Index Per Article: 13.0] [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: 06/19/2004] [Accepted: 09/02/2004] [Indexed: 11/09/2022]
Abstract
In higher organisms the formation of the steroid scaffold is catalysed exclusively by the membrane-bound oxidosqualene cyclase (OSC; lanosterol synthase). In a highly selective cyclization reaction OSC forms lanosterol with seven chiral centres starting from the linear substrate 2,3-oxidosqualene. Valuable data on the mechanism of the complex cyclization cascade have been collected during the past 50 years using suicide inhibitors, mutagenesis studies and homology modelling. Nevertheless it is still not fully understood how the enzyme catalyses the reaction. Because of the decisive role of OSC in cholesterol biosynthesis it represents a target for the discovery of novel anticholesteraemic drugs that could complement the widely used statins. Here we present two crystal structures of the human membrane protein OSC: the target protein with an inhibitor that showed cholesterol lowering in vivo opens the way for the structure-based design of new OSC inhibitors. The complex with the reaction product lanosterol gives a clear picture of the way in which the enzyme achieves product specificity in this highly exothermic cyclization reaction.
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Affiliation(s)
- Ralf Thoma
- F. Hoffmann-La Roche AG, Pharma Research Discovery Chemistry, 4070 Basel, Switzerland
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25
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Thoma R, D'Arcy B, Müller F, Kusznir E, Stihle M, Morand O, Ruf A. Crystal structure of oxido squalene cyclase. Acta Crystallogr A 2004. [DOI: 10.1107/s0108767304099520] [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: 11/11/2022] Open
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26
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Ruf A, Müller F, D'Arcy B, Stihle M, Kusznir E, Handschin C, Morand OH, Thoma R. The monotopic membrane protein human oxidosqualene cyclase is active as monomer. Biochem Biophys Res Commun 2004; 315:247-54. [PMID: 14766201 DOI: 10.1016/j.bbrc.2004.01.052] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [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: 01/13/2004] [Indexed: 12/16/2022]
Abstract
The monotopic integral membrane protein 2,3-oxidosqualene cyclase (OSC) catalyzes the formation of lanosterol the first sterol precursor of cholesterol in mammals. Therefore, it is an important target for the development of new hypocholesterolemic drugs. Here, we report the overexpression and purification of functional human OSC (hOSC) in Pichia pastoris. The obtained IC(50) for the reference inhibitor Ro 48-8071 is nearly identical for the recombinant hOSC compared to OSC from human liver microsomes. The correlation of analytical ultracentrifugation data and activity measurements showed the highest enzymatic activity for the monomeric hOSC indicating that this would be the natural form. Furthermore, these data helped us to identify the detergent for a successful crystallization of the protein. The availability of this active recombinant human membrane protein is a very important step on the way to a more detailed functional and structural characterization of OSCs.
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Affiliation(s)
- Armin Ruf
- F. Hoffmann-La Roche Ltd., Pharma Research Discovery, CH-4070 Basel, Switzerland
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27
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Thoma R, Löffler B, Stihle M, Huber W, Ruf A, Hennig M. Structural basis of proline-specific exopeptidase activity as observed in human dipeptidyl peptidase-IV. Structure 2003; 11:947-59. [PMID: 12906826 DOI: 10.1016/s0969-2126(03)00160-6] [Citation(s) in RCA: 166] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Inhibition of dipeptidyl peptidase IV (DPP-IV), the main glucagon-like peptide 1 (GLP1)-degrading enzyme, has been proposed for the treatment of type II diabetes. We expressed and purified the ectodomain of human DPP-IV in Pichia pastoris and determined the X-ray structure at 2.1 A resolution. The enzyme consists of two domains, the catalytic domain, with an alpha/beta hydrolase fold, and a beta propeller domain with an 8-fold repeat of a four-strand beta sheet motif. The beta propeller domain contributes two important functions to the molecule that have not been reported for such structures, an extra beta sheet motif that forms part of the dimerization interface and an additional short helix with a double Glu sequence motif. The Glu motif provides recognition and a binding site for the N terminus of the substrates, as revealed by the complex structure with diprotin A, a substrate with low turnover that is trapped in the tetrahedral intermediate of the reaction in the crystal.
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Affiliation(s)
- Ralf Thoma
- F. Hoffmann-La Roche AG, Pharma Research Discovery, 4070 Basel, Switzerland
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28
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Olsen JA, Banner DW, Seiler P, Obst Sander U, D'Arcy A, Stihle M, Müller K, Diederich F. A fluorine scan of thrombin inhibitors to map the fluorophilicity/fluorophobicity of an enzyme active site: evidence for C-F...C=O interactions. Angew Chem Int Ed Engl 2003; 42:2507-11. [PMID: 12800172 DOI: 10.1002/anie.200351268] [Citation(s) in RCA: 171] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jacob A Olsen
- Laboratorium für Organische Chemie, ETH-Hönggerberg, HCI, 8093 Zürich, Switzerland
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D'Arcy A, Mac Sweeney A, Stihle M, Haber A. The advantages of using a modified microbatch method for rapid screening of protein crystallization conditions. Acta Crystallogr D Biol Crystallogr 2003; 59:396-9. [PMID: 12554964 DOI: 10.1107/s0907444902022011] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2002] [Accepted: 11/26/2002] [Indexed: 11/10/2022]
Abstract
In this study, characterization and optimization of a modified microbatch crystallization technique has been attempted in order to provide a rapid screening method. Using this method for screening has certain advantages over standard vapour-diffusion methods: no sealing of drops is required, no reservoir solutions are needed and the experiments can easily be performed over a range of temperatures.
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Thoma R, Schlatter D, Stihle M, Kueng E, Mueller F, Boroni E, Hennig M. Crystal engineering yields crystals of cyclophilin D diffracting to 1.5 Å resolution. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302096095] [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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32
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Hennig M, Schlatter D, Stihle M, Thoma R. Crystal engineering yields crystals of cyclophilin D diffracting to 1.5 Å resolution: a sound basis for the support of drug discovery. Acta Crystallogr A 2002. [DOI: 10.1107/s010876730209654x] [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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33
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D'Arcy A, Stihle M, Kostrewa D, Dale G. Crystal engineering: a case study using the 24 kDa fragment of the DNA gyrase B subunit from Escherichia coli. Acta Crystallogr D Biol Crystallogr 1999; 55:1623-5. [PMID: 10489468 DOI: 10.1107/s0907444999008136] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Site-directed mutagenesis was used to determine the efficacy of changing surface residues to improve crystal quality. Nine mutants of the 24 kDa fragment of the Escherichia coli DNA gyrase B subunit were produced, changing residues on the protein's surface. The mutations changed either the charge or the polarity of the wild-type amino acid. It was found that single amino-acid changes on the surface could have a dramatic effect on the crystallization properties of the protein and generally resulted in an improvement in the number of crystal-screen hits as well as an improvement in crystal quality. It is concluded that crystal engineering is a valuable tool for protein crystallography.
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Affiliation(s)
- A D'Arcy
- F. Hoffmann-La Roche Ltd Pharmaceutical Research, Chemical Technologies, CH-4070, Basel, Switzerland
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