1
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Baltgalvis KA, Lamb KN, Symons KT, Wu CC, Hoffman MA, Snead AN, Song X, Glaza T, Kikuchi S, Green JC, Rogness DC, Lam B, Rodriguez-Aguirre ME, Woody DR, Eissler CL, Rodiles S, Negron SM, Bernard SM, Tran E, Pollock J, Tabatabaei A, Contreras V, Williams HN, Pastuszka MK, Sigler JJ, Pettazzoni P, Rudolph MG, Classen M, Brugger D, Claiborne C, Plancher JM, Cuartas I, Seoane J, Burgess LE, Abraham RT, Weinstein DS, Simon GM, Patricelli MP, Kinsella TM. Chemoproteomic discovery of a covalent allosteric inhibitor of WRN helicase. Nature 2024; 629:435-442. [PMID: 38658751 DOI: 10.1038/s41586-024-07318-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/19/2023] [Accepted: 03/14/2024] [Indexed: 04/26/2024]
Abstract
WRN helicase is a promising target for treatment of cancers with microsatellite instability (MSI) due to its essential role in resolving deleterious non-canonical DNA structures that accumulate in cells with faulty mismatch repair mechanisms1-5. Currently there are no approved drugs directly targeting human DNA or RNA helicases, in part owing to the challenging nature of developing potent and selective compounds to this class of proteins. Here we describe the chemoproteomics-enabled discovery of a clinical-stage, covalent allosteric inhibitor of WRN, VVD-133214. This compound selectively engages a cysteine (C727) located in a region of the helicase domain subject to interdomain movement during DNA unwinding. VVD-133214 binds WRN protein cooperatively with nucleotide and stabilizes compact conformations lacking the dynamic flexibility necessary for proper helicase function, resulting in widespread double-stranded DNA breaks, nuclear swelling and cell death in MSI-high (MSI-H), but not in microsatellite-stable, cells. The compound was well tolerated in mice and led to robust tumour regression in multiple MSI-H colorectal cancer cell lines and patient-derived xenograft models. Our work shows an allosteric approach for inhibition of WRN function that circumvents competition from an endogenous ATP cofactor in cancer cells, and designates VVD-133214 as a promising drug candidate for patients with MSI-H cancers.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Betty Lam
- Vividion Therapeutics, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Piergiorgio Pettazzoni
- Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Markus G Rudolph
- Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Moritz Classen
- Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Doris Brugger
- Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Christopher Claiborne
- Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Jean-Marc Plancher
- Pharma Research and Early Development pRED F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Isabel Cuartas
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Joan Seoane
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | | | - Robert T Abraham
- Vividion Therapeutics, San Diego, CA, USA
- Odyssey Therapeutics, San Diego, CA, USA
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2
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Krummenacher D, He W, Kuhn B, Schnider C, Beurier A, Brom V, Sivasothy T, Marty C, Tosstorff A, Hewings DS, Mesch S, Pinard E, Brändlin M, Hochstrasser R, Westwood P, Rothe J, Kronenberger A, Morandi F, Gutbier S, Schuler A, Heer D, Gloria LE, Joedicke L, Rudolph MG, Müller L, Grüninger F, Baumann K, Kaniyappan S, Manevski N, Bartels B. Discovery of Orally Available and Brain Penetrant AEP Inhibitors. J Med Chem 2023; 66:17026-17043. [PMID: 38090813 DOI: 10.1021/acs.jmedchem.3c01804] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 12/29/2023]
Abstract
Alzheimer's Disease (AD) is the most widespread form of dementia, with one of the pathological hallmarks being the formation of neurofibrillary tangles (NFTs). These tangles consist of phosphorylated Tau fragments. Asparagine endopeptidase (AEP) is a key Tau cleaving enzyme that generates aggregation-prone Tau fragments. Inhibition of AEP to reduce the level of toxic Tau fragment formation could represent a promising therapeutic strategy. Here, we report the first orthosteric, selective, orally bioavailable, and brain penetrant inhibitors with an irreversible binding mode. We outline the development of the series starting from reversible molecules and demonstrate the link between inhibition of AEP and reduction of Tau N368 fragment both in vitro and in vivo.
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Affiliation(s)
- Daniela Krummenacher
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Weiping He
- WuXi AppTec (Wuhan) Co. Ltd., Wuhan East Lake High-Tech Development Zone, 666 GaoXin Road, Wuhan, Hubei 430075, China
| | - Bernd Kuhn
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Christian Schnider
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Angélica Beurier
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Virginie Brom
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Thulase Sivasothy
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Christine Marty
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Andreas Tosstorff
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - David S Hewings
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Stefanie Mesch
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Emmanuel Pinard
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Mathis Brändlin
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Remo Hochstrasser
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Paul Westwood
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Judith Rothe
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Alexandra Kronenberger
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Federica Morandi
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Simon Gutbier
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Angelika Schuler
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Dominik Heer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Ludivine Esteves Gloria
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Lisa Joedicke
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Markus G Rudolph
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Lutz Müller
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Fiona Grüninger
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Karlheinz Baumann
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Senthilvelrajan Kaniyappan
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Nenad Manevski
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Björn Bartels
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
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3
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Kuhn B, Peters JU, Rudolph MG, Mohr P, Stahl M, Tosstorff A. Details Matter in Structure-based Drug Design. Chimia (Aarau) 2023; 77:489-493. [PMID: 38047790 DOI: 10.2533/chimia.2023.489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/15/2023] [Indexed: 12/05/2023] Open
Abstract
Successful structure-based drug design (SBDD) requires the optimization of interactions with the target protein and the minimization of ligand strain. Both factors are often modulated by small changes in the chemical structure which can lead to profound changes in the preferred conformation and interaction preferences of the ligand. We draw from examples of a Roche project targeting phosphodiesterase 10 to highlight that details matter in SBDD. Data mining in crystal structure databases can help to identify these sometimes subtle effects, but it is also a great resource to learn about molecular recognition in general and can be used as part of molecular design tools. We illustrate the use of the Cambridge Structural Database for identifying preferred structural motifs for intramolecular hydrogen bonding and of the Protein Data Bank for deriving propensities for protein-ligand interactions.
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Affiliation(s)
- Bernd Kuhn
- Roche Pharma Research and Early Development, Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland.
| | - Jens-Uwe Peters
- Roche Pharma Research and Early Development, Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland.
| | - Markus G Rudolph
- Roche Pharma Research and Early Development, Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland.
| | - Peter Mohr
- Roche Pharma Research and Early Development, Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland.
| | - Martin Stahl
- Roche Pharma Research and Early Development, Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland.
| | - Andreas Tosstorff
- Roche Pharma Research and Early Development, Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland.
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4
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Cumming JG, Kreis L, Kühne H, Wermuth R, Vercruysse M, Kramer C, Rudolph MG, Xu Z. Discovery of a Series of Indane-Containing NBTIs with Activity against Multidrug-Resistant Gram-Negative Pathogens. ACS Med Chem Lett 2023; 14:993-998. [PMID: 37465290 PMCID: PMC10350941 DOI: 10.1021/acsmedchemlett.3c00187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
The rise of multidrug-resistant (MDR) Gram-negative bacteria is a major global health problem necessitating the discovery of new classes of antibiotics. Novel bacterial topoisomerase inhibitors (NBTIs) target the clinically validated bacterial type II topoisomerases with a distinct binding site and mechanism of action to fluoroquinolone antibiotics, thus avoiding cross-resistance to this drug class. Here we report the discovery of a series of NBTIs incorporating a novel indane DNA binding moiety. X-ray cocrystal structures of compounds 2 and 17a bound to Staphylococcus aureus DNA gyrase-DNA were determined, revealing specific interactions with the enzyme binding pocket at the GyrA dimer interface and a long-range electrostatic interaction between the basic amine in the linker and the carboxylate of Asp83. Exploration of the structure-activity relationship within the series led to the identification of lead compound 18c, which showed potent broad-spectrum activity against a panel of MDR Gram-negative bacteria.
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Affiliation(s)
- John G. Cumming
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Lukas Kreis
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Holger Kühne
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Roger Wermuth
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Maarten Vercruysse
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Christian Kramer
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Markus G. Rudolph
- Roche
Pharma Research & Early Development, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Zhiheng Xu
- China
Innovation Center of Roche, Roche R&D
Center (China) Ltd., Shanghai 201203, China
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5
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Mhaindarkar VP, Rasche R, Kümmel D, Rudolph MG, Klostermeier D. Structure of reverse gyrase with a minimal latch that supports ATP-dependent positive supercoiling without specific interactions with the topoisomerase domain. Acta Crystallogr D Struct Biol 2023:S2059798323002565. [PMID: 37204816 DOI: 10.1107/s2059798323002565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
Reverse gyrase is the only topoisomerase that introduces positive supercoils into DNA in an ATP-dependent reaction. Positive DNA supercoiling becomes possible through the functional cooperation of the N-terminal helicase domain of reverse gyrase with its C-terminal type IA topoisomerase domain. This cooperation is mediated by a reverse-gyrase-specific insertion into the helicase domain termed the `latch'. The latch consists of a globular domain inserted at the top of a β-bulge loop that connects this globular part to the helicase domain. While the globular domain shows little conservation in sequence and length and is dispensable for DNA supercoiling, the β-bulge loop is required for supercoiling activity. It has previously been shown that the β-bulge loop constitutes a minimal latch that couples ATP-dependent processes in the helicase domain to DNA processing by the topoisomerase domain. Here, the crystal structure of Thermotoga maritima reverse gyrase with such a β-bulge loop as a minimal latch is reported. It is shown that the β-bulge loop supports ATP-dependent DNA supercoiling of reverse gyrase without engaging in specific interactions with the topoisomerase domain. When only a small latch or no latch is present, a helix in the nearby helicase domain of T. maritima reverse gyrase partially unfolds. Comparison of the sequences and predicted structures of latch regions in other reverse gyrases shows that neither sequence nor structure are decisive factors for latch functionality; instead, the decisive factors are likely to be electrostatics and plain steric bulk.
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Affiliation(s)
- Vaibhav P Mhaindarkar
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - René Rasche
- Institute for Biochemistry, University of Muenster, Corrensstrasse 36, 48149 Muenster, Germany
| | - Daniel Kümmel
- Institute for Biochemistry, University of Muenster, Corrensstrasse 36, 48149 Muenster, Germany
| | - Markus G Rudolph
- Pharma Research and Early Development, Molecular Design and Chemical Biology, Hoffmann-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
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6
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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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7
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Richter K, Rufer AC, Muller M, Burger D, Casagrande F, Grossenbacher T, Huber S, Hug MN, Koldewey P, D'Osualdo A, Schlatter D, Stoll T, Rudolph MG. Reply to Alarcon and Borroto: Small molecule AX-024 reduces T cell proliferation independently of CD3ε-Nck1 interaction at SH3.1. J Biol Chem 2020; 295:10077. [PMID: 32680972 DOI: 10.1074/jbc.rl120.014441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Kirsten Richter
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Arne C Rufer
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Magali Muller
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Dominique Burger
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Fabio Casagrande
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Tabea Grossenbacher
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Sylwia Huber
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Melanie N Hug
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Philipp Koldewey
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Andrea D'Osualdo
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Daniel Schlatter
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Theodor Stoll
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Markus G Rudolph
- pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
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8
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Jaeger K, Bruenle S, Weinert T, Guba W, Muehle J, Miyazaki T, Weber M, Furrer A, Haenggi N, Tetaz T, Huang CY, Mattle D, Vonach JM, Gast A, Kuglstatter A, Rudolph MG, Nogly P, Benz J, Dawson RJP, Standfuss J. Structural Basis for Allosteric Ligand Recognition in the Human CC Chemokine Receptor 7. Cell 2020; 178:1222-1230.e10. [PMID: 31442409 PMCID: PMC6709783 DOI: 10.1016/j.cell.2019.07.028] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/19/2019] [Accepted: 07/12/2019] [Indexed: 11/15/2022]
Abstract
The CC chemokine receptor 7 (CCR7) balances immunity and tolerance by homeostatic trafficking of immune cells. In cancer, CCR7-mediated trafficking leads to lymph node metastasis, suggesting the receptor as a promising therapeutic target. Here, we present the crystal structure of human CCR7 fused to the protein Sialidase NanA by using data up to 2.1 Å resolution. The structure shows the ligand Cmp2105 bound to an intracellular allosteric binding pocket. A sulfonamide group, characteristic for various chemokine receptor ligands, binds to a patch of conserved residues in the Gi protein binding region between transmembrane helix 7 and helix 8. We demonstrate how structural data can be used in combination with a compound repository and automated thermal stability screening to identify and modulate allosteric chemokine receptor antagonists. We detect both novel (CS-1 and CS-2) and clinically relevant (CXCR1-CXCR2 phase-II antagonist Navarixin) CCR7 modulators with implications for multi-target strategies against cancer.
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Affiliation(s)
- Kathrin Jaeger
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI
| | - Steffen Bruenle
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI
| | - Wolfgang Guba
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Jonas Muehle
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI; Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Takuya Miyazaki
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland; Chugai Pharmaceutical Co., Ltd., Research Division, Kamakura Research Labs, Kamakura, Kanagawa, Japan
| | - Martin Weber
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Antonia Furrer
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI
| | - Noemi Haenggi
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Tim Tetaz
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Chia-Ying Huang
- Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Daniel Mattle
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI; Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Jean-Marie Vonach
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Alain Gast
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Andreas Kuglstatter
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Markus G Rudolph
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Przemyslaw Nogly
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI
| | - Joerg Benz
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Roger J P Dawson
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland.
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI.
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9
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Richter K, Rufer AC, Muller M, Burger D, Casagrande F, Grossenbacher T, Huber S, Hug MN, Koldewey P, D'Osualdo A, Schlatter D, Stoll T, Rudolph MG. Small molecule AX-024 reduces T cell proliferation independently of CD3ϵ/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain. J Biol Chem 2020; 295:7849-7864. [PMID: 32317279 PMCID: PMC7278359 DOI: 10.1074/jbc.ra120.012788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
Activation of the T cell receptor (TCR) results in binding of the adapter protein Nck (noncatalytic region of tyrosine kinase) to the CD3ϵ subunit of the TCR. The interaction was suggested to be important for the amplification of TCR signals and is governed by a proline-rich sequence (PRS) in CD3ϵ that binds to the first Src homology 3 (SH3) domain of Nck (Nck-SH3.1). Inhibition of this protein/protein interaction ameliorated inflammatory symptoms in mouse models of multiple sclerosis, psoriasis, and asthma. A small molecule, AX-024, was reported to inhibit the Nck/CD3ϵ interaction by physically binding to the Nck1-SH3.1 domain, suggesting a route to develop an inhibitor of the Nck1/CD3ϵ interaction for modulating TCR activity in autoimmune and inflammatory diseases. We show here that AX-024 reduces T cell proliferation upon weak TCR stimulation but does not significantly affect phosphorylation of Zap70 (ζ chain of T cell receptor–associated protein kinase 70). We also find that AX-024 is likely not involved in modulating the Nck/TCR interaction but probably has other targets in T cells. An array of biophysical techniques did not detect a direct interaction between AX-024 and Nck-SH3.1 in vitro. Crystal structures of the Nck-SH3.1 domain revealed its binding mode to the PRS in CD3ϵ. The SH3 domain tends to generate homodimers through a domain swap. Domain swaps observed previously in other SH3 domains indicate a general propensity of this protein fold to exchange structural elements. The swapped form of Nck-SH3.1 is unable to bind CD3ϵ, possibly representing an inactive form of Nck in cells.
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Affiliation(s)
- Kirsten Richter
- I2O Disease Translational Area, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Arne C Rufer
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Magali Muller
- I2O Disease Translational Area, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Dominique Burger
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Fabio Casagrande
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Tabea Grossenbacher
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Sylwia Huber
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Melanie N Hug
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Philipp Koldewey
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Andrea D'Osualdo
- I2O Disease Translational Area, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Daniel Schlatter
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Theodor Stoll
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus G Rudolph
- Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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10
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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
![]()
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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11
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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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12
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Mattle D, Kuhn B, Aebi J, Bedoucha M, Kekilli D, Grozinger N, Alker A, Rudolph MG, Schmid G, Schertler GFX, Hennig M, Standfuss J, Dawson RJP. Ligand channel in pharmacologically stabilized rhodopsin. Proc Natl Acad Sci U S A 2018; 115:3640-3645. [PMID: 29555765 PMCID: PMC5889642 DOI: 10.1073/pnas.1718084115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In the degenerative eye disease retinitis pigmentosa (RP), protein misfolding leads to fatal consequences for cell metabolism and rod and cone cell survival. To stop disease progression, a therapeutic approach focuses on stabilizing inherited protein mutants of the G protein-coupled receptor (GPCR) rhodopsin using pharmacological chaperones (PC) that improve receptor folding and trafficking. In this study, we discovered stabilizing nonretinal small molecules by virtual and thermofluor screening and determined the crystal structure of pharmacologically stabilized opsin at 2.4 Å resolution using one of the stabilizing hits (S-RS1). Chemical modification of S-RS1 and further structural analysis revealed the core binding motif of this class of rhodopsin stabilizers bound at the orthosteric binding site. Furthermore, previously unobserved conformational changes are visible at the intradiscal side of the seven-transmembrane helix bundle. A hallmark of this conformation is an open channel connecting the ligand binding site with the membrane and the intradiscal lumen of rod outer segments. Sufficient in size, the passage permits the exchange of hydrophobic ligands such as retinal. The results broaden our understanding of rhodopsin's conformational flexibility and enable therapeutic drug intervention against rhodopsin-related retinitis pigmentosa.
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Affiliation(s)
- Daniel Mattle
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Bernd Kuhn
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Johannes Aebi
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Marc Bedoucha
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Demet Kekilli
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Nathalie Grozinger
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Andre Alker
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Markus G Rudolph
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Georg Schmid
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Gebhard F X Schertler
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Michael Hennig
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland;
| | - Roger J P Dawson
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland;
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13
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Klostermeier D, Rudolph MG. X-ray Crystallography. Biophys Chem 2018. [DOI: 10.1201/9781315156910-26] [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]
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14
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Klostermeier D, Rudolph MG. Nucleic Acids. Biophys Chem 2018. [DOI: 10.1201/9781315156910-20] [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]
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15
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Klostermeier D, Rudolph MG. Reaction Velocities and Rate Laws. Biophys Chem 2018. [DOI: 10.1201/9781315156910-8] [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]
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16
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Klostermeier D, Rudolph MG. Proteins. Biophys Chem 2018. [DOI: 10.1201/9781315156910-19] [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]
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17
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Klostermeier D, Rudolph MG. Imaging and Microscopy. Biophys Chem 2018. [DOI: 10.1201/9781315156910-27] [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]
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18
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Klostermeier D, Rudolph MG. Solution Scattering. Biophys Chem 2018. [DOI: 10.1201/9781315156910-25] [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]
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19
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Klostermeier D, Rudolph MG. Temperature Dependence of Rate Constants. Biophys Chem 2018. [DOI: 10.1201/9781315156910-15] [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]
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20
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Klostermeier D, Rudolph MG. Force Measurements. Biophys Chem 2018. [DOI: 10.1201/9781315156910-28] [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]
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21
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Klostermeier D, Rudolph MG. Systems and Their Surroundings. Biophys Chem 2018. [DOI: 10.1201/9781315156910-2] [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]
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22
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Klostermeier D, Rudolph MG. State Functions and the Laws of Thermodynamics. Biophys Chem 2018. [DOI: 10.1201/9781315156910-3] [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: 11/12/2022]
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23
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Klostermeier D, Rudolph MG. Binding Reactions One-Step and Two-Step Binding. Biophys Chem 2018. [DOI: 10.1201/9781315156910-12] [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]
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24
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Klostermeier D, Rudolph MG. Energetics and Chemical Equilibria. Biophys Chem 2018. [DOI: 10.1201/9781315156910-4] [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]
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25
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Klostermeier D, Rudolph MG. Magnetic Resonance. Biophys Chem 2018. [DOI: 10.1201/9781315156910-24] [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]
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26
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Klostermeier D, Rudolph MG. Optical Spectroscopy. Biophys Chem 2018. [DOI: 10.1201/9781315156910-23] [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]
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27
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Klostermeier D, Rudolph MG. Calorimetry. Biophys Chem 2018. [DOI: 10.1201/9781315156910-31] [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]
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28
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Klostermeier D, Rudolph MG. Thermodynamics of Transport Processes. Biophys Chem 2018. [DOI: 10.1201/9781315156910-5] [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]
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29
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Klostermeier D, Rudolph MG. Steady-State (Enzyme) Kinetics. Biophys Chem 2018. [DOI: 10.1201/9781315156910-13] [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]
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30
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Klostermeier D, Rudolph MG. Reaction Types. Biophys Chem 2018. [DOI: 10.1201/9781315156910-10] [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]
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31
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Klostermeier D, Rudolph MG. Integrated Rate Laws for Uni- and Bimolecular Reactions. Biophys Chem 2018. [DOI: 10.1201/9781315156910-9] [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]
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32
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Klostermeier D, Rudolph MG. Prefixes, Units, Constants. Biophys Chem 2018. [DOI: 10.1201/9781315156910-32] [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]
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33
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Klostermeier D, Rudolph MG. Electrochemistry. Biophys Chem 2018. [DOI: 10.1201/9781315156910-6] [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]
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Klostermeier D, Rudolph MG. Principles of Catalysis. Biophys Chem 2018. [DOI: 10.1201/9781315156910-16] [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]
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35
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Klostermeier D, Rudolph MG. Complex Reaction Schemes and Their Analysis. Biophys Chem 2018. [DOI: 10.1201/9781315156910-14] [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]
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Klostermeier D, Rudolph MG. Molecular Structure and Interactions. Biophys Chem 2018. [DOI: 10.1201/9781315156910-18] [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]
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Klostermeier D, Rudolph MG. Molecular Mass, Size, and Shape. Biophys Chem 2018. [DOI: 10.1201/9781315156910-30] [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]
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Klostermeier D, Rudolph MG. Rate-Limiting Steps. Biophys Chem 2018. [DOI: 10.1201/9781315156910-11] [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]
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39
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Klostermeier D, Rudolph MG. Transient Kinetic Methods. Biophys Chem 2018. [DOI: 10.1201/9781315156910-29] [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]
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40
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Klostermeier D, Rudolph MG. Mathematical Concepts Used in This Book. Biophys Chem 2018. [DOI: 10.1201/9781315156910-33] [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]
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41
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Klostermeier D, Rudolph MG. Computational Biology. Biophys Chem 2018. [DOI: 10.1201/9781315156910-21] [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]
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Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters P, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE. D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J Comput Aided Mol Des 2018; 32:1-20. [PMID: 29204945 PMCID: PMC5767524 DOI: 10.1007/s10822-017-0088-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/20/2017] [Indexed: 01/07/2023]
Abstract
The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures and affinities for the nuclear receptor farnesoid X receptor (FXR), contributed by F. Hoffmann-La Roche. The dataset contained 102 IC50 values, spanning six orders of magnitude, and 36 high-resolution co-crystal structures with representatives of four major ligand classes. Strong global participation was evident, with 49 participants submitting 262 prediction submission packages in total. Procedurally, GC2 mimicked Grand Challenge 2015 (GC2015), with a Stage 1 subchallenge testing ligand pose prediction methods and ranking and scoring methods, and a Stage 2 subchallenge testing only ligand ranking and scoring methods after the release of all blinded co-crystal structures. Two smaller curated sets of 18 and 15 ligands were developed to test alchemical free energy methods. This overview summarizes all aspects of GC2, including the dataset details, challenge procedures, and participant results. We also consider implications for progress in the field, while highlighting methodological areas that merit continued development. Similar to GC2015, the outcome of GC2 underscores the pressing need for methods development in pose prediction, particularly for ligand scaffolds not currently represented in the Protein Data Bank ( http://www.pdb.org ), and in affinity ranking and scoring of bound ligands.
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Affiliation(s)
- Zied Gaieb
- Drug Design Data Resource, University of California, San Diego, La Jolla, CA 92093
| | - Shuai Liu
- Silicon Therapeutics, Boston MA 02210
| | | | - Michael Chiu
- Drug Design Data Resource, University of California, San Diego, La Jolla, CA 92093
| | - Huanwang Yang
- RCSB Protein Data Bank Rutgers University, New Brunswick, NJ 08901
| | - Chenghua Shao
- RCSB Protein Data Bank Rutgers University, New Brunswick, NJ 08901
| | - Victoria A. Feher
- Drug Design Data Resource, University of California, San Diego, La Jolla, CA 92093
| | | | - Bernd Kuhn
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus G. Rudolph
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | | | - Michael K. Gilson
- Drug Design Data Resource, University of California, San Diego, La Jolla, CA 92093,Correspondence to:
| | - Rommie E. Amaro
- Drug Design Data Resource, University of California, San Diego, La Jolla, CA 92093,Correspondence to:
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Steffen W, Ko FC, Patel J, Lyamichev V, Albert TJ, Benz J, Rudolph MG, Bergmann F, Streidl T, Kratzsch P, Boenitz-Dulat M, Oelschlaegel T, Schraeml M. Discovery of a microbial transglutaminase enabling highly site-specific labeling of proteins. J Biol Chem 2017; 292:15622-15635. [PMID: 28751378 PMCID: PMC5612097 DOI: 10.1074/jbc.m117.797811] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/26/2017] [Indexed: 12/21/2022] Open
Abstract
Microbial transglutaminases (MTGs) catalyze the formation of Gln–Lys isopeptide bonds and are widely used for the cross-linking of proteins and peptides in food and biotechnological applications (e.g. to improve the texture of protein-rich foods or in generating antibody-drug conjugates). Currently used MTGs have low substrate specificity, impeding their biotechnological use as enzymes that do not cross-react with nontarget substrates (i.e. as bio-orthogonal labeling systems). Here, we report the discovery of an MTG from Kutzneria albida (KalbTG), which exhibited no cross-reactivity with known MTG substrates or commonly used target proteins, such as antibodies. KalbTG was produced in Escherichia coli as soluble and active enzyme in the presence of its natural inhibitor ammonium to prevent potentially toxic cross-linking activity. The crystal structure of KalbTG revealed a conserved core similar to other MTGs but very short surface loops, making it the smallest MTG characterized to date. Ultra-dense peptide array technology involving a pool of 1.4 million unique peptides identified specific recognition motifs for KalbTG in these peptides. We determined that the motifs YRYRQ and RYESK are the best Gln and Lys substrates of KalbTG, respectively. By first reacting a bifunctionalized peptide with the more specific KalbTG and in a second step with the less specific MTG from Streptomyces mobaraensis, a successful bio-orthogonal labeling system was demonstrated. Fusing the KalbTG recognition motif to an antibody allowed for site-specific and ratio-controlled labeling using low label excess. Its site specificity, favorable kinetics, ease of use, and cost-effective production render KalbTG an attractive tool for a broad range of applications, including production of therapeutic antibody-drug conjugates.
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Affiliation(s)
- Wojtek Steffen
- From Roche Diagnostics GmbH, CPS, Nonnenwald 2, 82377 Penzberg, Germany,
| | - Fu Chong Ko
- From Roche Diagnostics GmbH, CPS, Nonnenwald 2, 82377 Penzberg, Germany
| | - Jigar Patel
- Roche Sequencing, NimbleGen, Madison, Wisconsin 53719, and
| | | | | | - Jörg Benz
- F. Hoffmann-La Roche Ltd., pRED, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus G Rudolph
- F. Hoffmann-La Roche Ltd., pRED, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Frank Bergmann
- From Roche Diagnostics GmbH, CPS, Nonnenwald 2, 82377 Penzberg, Germany
| | - Thomas Streidl
- From Roche Diagnostics GmbH, CPS, Nonnenwald 2, 82377 Penzberg, Germany
| | - Peter Kratzsch
- From Roche Diagnostics GmbH, CPS, Nonnenwald 2, 82377 Penzberg, Germany
| | | | | | - Michael Schraeml
- From Roche Diagnostics GmbH, CPS, Nonnenwald 2, 82377 Penzberg, Germany
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Lerner C, Jakob-Roetne R, Buettelmann B, Ehler A, Rudolph MG, Rodríguez Sarmiento RM. Correction to Design of Potent and Druglike Nonphenolic Inhibitors for Catechol O-Methyltransferase Derived from a Fragment Screening Approach Targeting the S-Adenosyl- l-methionine Pocket. J Med Chem 2017; 60:4099. [DOI: 10.1021/acs.jmedchem.7b00613] [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: 11/29/2022]
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45
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Favuzza P, Guffart E, Tamborrini M, Scherer B, Dreyer AM, Rufer AC, Erny J, Hoernschemeyer J, Thoma R, Schmid G, Gsell B, Lamelas A, Benz J, Joseph C, Matile H, Pluschke G, Rudolph MG. Structure of the malaria vaccine candidate antigen CyRPA and its complex with a parasite invasion inhibitory antibody. eLife 2017; 6. [PMID: 28195038 PMCID: PMC5349852 DOI: 10.7554/elife.20383] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 02/06/2017] [Indexed: 12/02/2022] Open
Abstract
Invasion of erythrocytes by Plasmodial merozoites is a composite process involving the interplay of several proteins. Among them, the Plasmodium falciparum Cysteine-Rich Protective Antigen (PfCyRPA) is a crucial component of a ternary complex, including Reticulocyte binding-like Homologous protein 5 (PfRH5) and the RH5-interacting protein (PfRipr), essential for erythrocyte invasion. Here, we present the crystal structures of PfCyRPA and its complex with the antigen-binding fragment of a parasite growth inhibitory antibody. PfCyRPA adopts a 6-bladed β-propeller structure with similarity to the classic sialidase fold, but it has no sialidase activity and fulfills a purely non-enzymatic function. Characterization of the epitope recognized by protective antibodies may facilitate design of peptidomimetics to focus vaccine responses on protective epitopes. Both in vitro and in vivo anti-PfCyRPA and anti-PfRH5 antibodies showed more potent parasite growth inhibitory activity in combination than on their own, supporting a combined delivery of PfCyRPA and PfRH5 in vaccines. DOI:http://dx.doi.org/10.7554/eLife.20383.001 Malaria is one of the deadliest infectious diseases worldwide, killing over 400,000 people a year. About 200 million people are infected every year, placing a huge social and medical burden especially on developing countries. Microscopic parasites known as Plasmodium are responsible for causing this disease. Plasmodium parasites have a complex life cycle involving both mosquito and mammal hosts. This includes a stage where the parasites infect the mammal’s red blood cells, which causes the symptoms of the disease. In 2012, a team of researchers discovered that a protein called CyRPA forms a group (or ‘complex’) with several other proteins to allow the parasites to enter red blood cells. Developing a vaccine is one of the most promising approaches to prevent malaria. Vaccines help the body to recognise and fight an invading microbe by triggering an immune response that results in the production of proteins called antibodies, which can bind to specific molecules on the surface of the microbe. If the microbe later enters the body, these antibodies can be produced quickly to eliminate the microbe before it causes disease. However, efforts to develop a highly effective vaccine against malaria have so far been unsuccessful. Favuzza et al. – including some of the researchers involved in the 2012 work – used a technique called X-ray crystallography to investigate the three-dimensional structure of the CyRPA protein. The experiments show that an antibody is able to bind to a region of CyRPA – a designated ‘protective epitope’ – that is similar in the CyRPA proteins of all Plasmodium falciparum strains. These antibodies can prevent the parasite from entering the red blood cells, and vaccines containing CyRPA may therefore be effective at protecting individuals from malaria. The findings of Favuzza et al. also suggest that using CyRPA in combination with another protein in the complex called RH5 could make the vaccine more powerful as it would make it harder for the parasite to become resistant. The next step following on from this work is to design a vaccine containing protective CyRPA epitopes that triggers an immune response in mammals that is strong enough to reduce the numbers of parasites in the blood. A future challenge will be to develop a vaccine that combines several proteins involved in different stages of the parasite’s life cycle to provide full protection against malaria. DOI:http://dx.doi.org/10.7554/eLife.20383.002
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Affiliation(s)
- Paola Favuzza
- Medical Parasitology and Infection Biology Department, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Elena Guffart
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Marco Tamborrini
- Medical Parasitology and Infection Biology Department, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Bianca Scherer
- Medical Parasitology and Infection Biology Department, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Anita M Dreyer
- Medical Parasitology and Infection Biology Department, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Arne C Rufer
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Johannes Erny
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Joerg Hoernschemeyer
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Ralf Thoma
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Georg Schmid
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Bernard Gsell
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Araceli Lamelas
- Medical Parasitology and Infection Biology Department, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Joerg Benz
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Catherine Joseph
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Hugues Matile
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Gerd Pluschke
- Medical Parasitology and Infection Biology Department, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Markus G Rudolph
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
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Ruf A, Tetaz T, Schott B, Joseph C, Rudolph MG. Quadruple space-group ambiguity owing to rotational and translational noncrystallographic symmetry in human liver fructose-1,6-bisphosphatase. Acta Crystallogr D Struct Biol 2016; 72:1212-1224. [PMID: 27841754 PMCID: PMC5108348 DOI: 10.1107/s2059798316016715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/18/2016] [Indexed: 11/17/2022] Open
Abstract
Fructose-1,6-bisphosphatase (FBPase) is a key regulator of gluconeogenesis and a potential drug target for type 2 diabetes. FBPase is a homotetramer of 222 symmetry with a major and a minor dimer interface. The dimers connected via the minor interface can rotate with respect to each other, leading to the inactive T-state and active R-state conformations of FBPase. Here, the first crystal structure of human liver FBPase in the R-state conformation is presented, determined at a resolution of 2.2 Å in a tetragonal setting that exhibits an unusual arrangement of noncrystallographic symmetry (NCS) elements. Self-Patterson function analysis and various intensity statistics revealed the presence of pseudo-translation and the absence of twinning. The space group is P41212, but structure determination was also possible in space groups P43212, P4122 and P4322. All solutions have the same arrangement of three C2-symmetric dimers spaced by 1/3 along an NCS axis parallel to the c axis located at (1/4, 1/4, z), which is therefore invisible in a self-rotation function analysis. The solutions in the four space groups are related to one another and emulate a body-centred lattice. If all NCS elements were crystallographic, the space group would be I4122 with a c axis three times shorter and a single FBPase subunit in the asymmetric unit. I4122 is a minimal, non-isomorphic supergroup of the four primitive tetragonal space groups, explaining the space-group ambiguity for this crystal.
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Affiliation(s)
- Armin Ruf
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Tim Tetaz
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Brigitte Schott
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Catherine Joseph
- 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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Kühne H, Obst-Sander U, Kuhn B, Conte A, Ceccarelli SM, Neidhart W, Rudolph MG, Ottaviani G, Gasser R, So SS, Li S, Zhang X, Gao L, Myers M. Design and synthesis of selective, dual fatty acid binding protein 4 and 5 inhibitors. Bioorg Med Chem Lett 2016; 26:5092-5097. [DOI: 10.1016/j.bmcl.2016.08.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/18/2016] [Accepted: 08/20/2016] [Indexed: 12/18/2022]
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48
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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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Rudolph MG, Klostermeier D. When core competence is not enough: functional interplay of the DEAD-box helicase core with ancillary domains and auxiliary factors in RNA binding and unwinding. Biol Chem 2016; 396:849-65. [PMID: 25720120 DOI: 10.1515/hsz-2014-0277] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/04/2015] [Indexed: 11/15/2022]
Abstract
DEAD-box helicases catalyze RNA duplex unwinding in an ATP-dependent reaction. Members of the DEAD-box helicase family consist of a common helicase core formed by two RecA-like domains. According to the current mechanistic model for DEAD-box mediated RNA unwinding, binding of RNA and ATP triggers a conformational change of the helicase core, and leads to formation of a compact, closed state. In the closed conformation, the two parts of the active site for ATP hydrolysis and of the RNA binding site, residing on the two RecA domains, become aligned. Closing of the helicase core is coupled to a deformation of the RNA backbone and destabilization of the RNA duplex, allowing for dissociation of one of the strands. The second strand remains bound to the helicase core until ATP hydrolysis and product release lead to re-opening of the core. The concomitant disruption of the RNA binding site causes dissociation of the second strand. The activity of the helicase core can be modulated by interaction partners, and by flanking N- and C-terminal domains. A number of C-terminal flanking regions have been implicated in RNA binding: RNA recognition motifs (RRM) typically mediate sequence-specific RNA binding, whereas positively charged, unstructured regions provide binding sites for structured RNA, without sequence-specificity. Interaction partners modulate RNA binding to the core, or bind to RNA regions emanating from the core. The functional interplay of the helicase core and ancillary domains or interaction partners in RNA binding and unwinding is not entirely understood. This review summarizes our current knowledge on RNA binding to the DEAD-box helicase core and the roles of ancillary domains and interaction partners in RNA binding and unwinding by DEAD-box proteins.
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50
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Kuhn B, Guba W, Hert J, Banner D, Bissantz C, Ceccarelli S, Haap W, Körner M, Kuglstatter A, Lerner C, Mattei P, Neidhart W, Pinard E, Rudolph MG, Schulz-Gasch T, Woltering T, Stahl M. A Real-World Perspective on Molecular Design. J Med Chem 2016; 59:4087-102. [PMID: 26878596 DOI: 10.1021/acs.jmedchem.5b01875] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.
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Affiliation(s)
- Bernd Kuhn
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Wolfgang Guba
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jérôme Hert
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - David Banner
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Caterina Bissantz
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Simona Ceccarelli
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Wolfgang Haap
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Matthias Körner
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Andreas Kuglstatter
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Christian Lerner
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Patrizio Mattei
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Werner Neidhart
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Emmanuel Pinard
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus G Rudolph
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Tanja Schulz-Gasch
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Thomas Woltering
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Martin Stahl
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
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