1
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Altincekic N, Jores N, Löhr F, Richter C, Ehrhardt C, Blommers MJJ, Berg H, Öztürk S, Gande SL, Linhard V, Orts J, Abi Saad MJ, Bütikofer M, Kaderli J, Karlsson BG, Brath U, Hedenström M, Gröbner G, Sauer UH, Perrakis A, Langer J, Banci L, Cantini F, Fragai M, Grifagni D, Barthel T, Wollenhaupt J, Weiss MS, Robertson A, Bax A, Sreeramulu S, Schwalbe H. Targeting the Main Protease (M pro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies. ACS Chem Biol 2024; 19:563-574. [PMID: 38232960 PMCID: PMC10877576 DOI: 10.1021/acschembio.3c00720] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 01/19/2024]
Abstract
The main protease Mpro, nsp5, of SARS-CoV-2 (SCoV2) is one of its most attractive drug targets. Here, we report primary screening data using nuclear magnetic resonance spectroscopy (NMR) of four different libraries and detailed follow-up synthesis on the promising uracil-containing fragment Z604 derived from these libraries. Z604 shows time-dependent binding. Its inhibitory effect is sensitive to reducing conditions. Starting with Z604, we synthesized and characterized 13 compounds designed by fragment growth strategies. Each compound was characterized by NMR and/or activity assays to investigate their interaction with Mpro. These investigations resulted in the four-armed compound 35b that binds directly to Mpro. 35b could be cocrystallized with Mpro revealing its noncovalent binding mode, which fills all four active site subpockets. Herein, we describe the NMR-derived fragment-to-hit pipeline and its application for the development of promising starting points for inhibitors of the main protease of SCoV2.
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Affiliation(s)
- Nadide Altincekic
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Nathalie Jores
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Frank Löhr
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Institute
of Biophysical Chemistry, Goethe University
Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Christian Richter
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Claus Ehrhardt
- Department
of Biochemistry, University of Zurich, 8093 Zurich, Switzerland
| | | | - Hannes Berg
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Sare Öztürk
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Santosh L. Gande
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Verena Linhard
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Julien Orts
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Marie Jose Abi Saad
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Matthias Bütikofer
- Swiss
Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zürich, Switzerland
| | - Janina Kaderli
- Swiss
Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zürich, Switzerland
| | - B. Göran Karlsson
- Swedish
NMR Centre, Department of Chemistry and Molecular Biology, University of Gothenburg, SE40530 Göteborg, Sweden
- SciLifeLab, University of Gothenburg, SE40530 Göteborg, Sweden
| | - Ulrika Brath
- Swedish
NMR Centre, Department of Chemistry and Molecular Biology, University of Gothenburg, SE40530 Göteborg, Sweden
| | - Mattias Hedenström
- Swedish
NMR Centre, Department of Chemistry, University
of Umeå, SE-90187 Umeå, Sweden
| | - Gerhard Gröbner
- Swedish
NMR Centre, Department of Chemistry, University
of Umeå, SE-90187 Umeå, Sweden
| | - Uwe H. Sauer
- Protein
Production Sweden, Department of Chemistry, University of Umeå, SE-90187 Umeå, Sweden
| | - Anastassis Perrakis
- Oncode
Institute and Division of Biochemistry, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Julian Langer
- Max Planck Institute of
Biophysics, D-60438 Frankfurt am Main, Germany
| | - Lucia Banci
- Magnetic
Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche Metalloproteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Francesca Cantini
- Magnetic
Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche Metalloproteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic
Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche Metalloproteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Deborah Grifagni
- Magnetic
Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Tatjana Barthel
- Macromolecular
Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Jan Wollenhaupt
- Macromolecular
Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Manfred S. Weiss
- Macromolecular
Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | | | - Adriaan Bax
- NIH, LCP NIDDK, Bethesda, Maryland 20892, United States
| | - Sridhar Sreeramulu
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Harald Schwalbe
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
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2
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Hamway Y, Zimmermann K, Blommers MJJ, Sousa MV, Häberli C, Kulkarni S, Skalicky S, Hackl M, Götte M, Keiser J, da Costa CP, Spangenberg T, Azzaoui K. Modulation of Host-Parasite Interactions with Small Molecules Targeting Schistosoma mansoni microRNAs. ACS Infect Dis 2022; 8:2028-2034. [PMID: 36098656 PMCID: PMC9578036 DOI: 10.1021/acsinfecdis.2c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Parasites use different strategies of communication with their hosts. One communication channel that has been studied in recent years is the use of vesicle microRNAs to influence the host immune system by trematodes. sma-microRNA-10, secreted from Schistosoma mansoni, has been shown to influence the fate of host T-cells through manipulation of the NF-κB pathway. We have identified low molecular weight tool compounds that can interfere with this microRNA-mediated manipulation of the host immune system. We used a fragment-based screening approach by means of nuclear magnetic resonance (NMR) to identify binders to the precursor of the parasite sma-microRNA-10 present in their extracellular vesicles. The small fragments identified were used to select larger molecules. These molecules were shown to counteract the inhibition of NF-κB activity by sma-microRNA-10 in cell-based assays.
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Affiliation(s)
- Youssef Hamway
- Institute
for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, 81675Munich, Germany,Center
for Global Health, TUM School of Medicine, Technical University of Munich, 81675Munich, Germany
| | - Kaspar Zimmermann
- Saverna
Therapeutics AG, Gewerbestrasse
24, 4123Allschwil, Switzerland
| | | | - Mariana V. Sousa
- Institute
for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, 81675Munich, Germany,Center
for Global Health, TUM School of Medicine, Technical University of Munich, 81675Munich, Germany
| | - Cécile Häberli
- Department
of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123Allschwil, Switzerland,University
of Basel, Petersplatz
1, 4001Basel, Switzerland
| | - Shashank Kulkarni
- EMD
Serono Research & Development Institute, Inc. (a Business of Merck KGaA, Darmstadt, Germany), Billerica, Massachusetts01821, United States
| | | | | | - Marjo Götte
- Saverna
Therapeutics AG, Gewerbestrasse
24, 4123Allschwil, Switzerland
| | - Jennifer Keiser
- Department
of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123Allschwil, Switzerland,University
of Basel, Petersplatz
1, 4001Basel, Switzerland
| | - Clarissa Prazeres da Costa
- Institute
for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, 81675Munich, Germany,Center
for Global Health, TUM School of Medicine, Technical University of Munich, 81675Munich, Germany
| | - Thomas Spangenberg
- Global
Health Institute of Merck, Ares Trading S.A., a subsidiary of Merck KGaA, Darmstadt, Route de
Crassier 1, 1262Eysins, Switzerland,
| | - Kamal Azzaoui
- Saverna
Therapeutics AG, Gewerbestrasse
24, 4123Allschwil, Switzerland,
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3
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Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso ÍP, Felli IC, Da Poian AT, de Amorim GC, Fourkiotis NK, Gallo A, Ghosh D, Gomes-Neto F, Gorbatyuk O, Hao B, Kurauskas V, Lecoq L, Li Y, Mebus-Antunes NC, Mompean M, Neves-Martins TC, Ninot-Pedrosa M, Pinheiro AS, Pontoriero L, Pustovalova Y, Riek R, Robertson A, Abi Saad MJ, Treviño MA, Tsika AC, Almeida FC, Bax A, Henzler-Wildman K, Hoch JC, Jaudzems K, Laurents DV, Orts J, Pieratelli R, Spyroulias GA, Duchardt-Ferner E, Ferner J, Fuertig B, Hengesbach M, Löhr F, Qureshi N, Richter C, Saxena K, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Woehnert J, Schwalbe H. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205858] [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: 11/09/2022]
Affiliation(s)
- Hannes Berg
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Nadide Altincekic
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Islam Alshamleh
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Jasleen Kaur Bains
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julius Blechar
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Betül Ceylan
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Vanessa de Jesus
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Christin Fuks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Santosh L. Gande
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Bruno Hargittay
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Marie T. Hutchinson
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Robin Krishnathas
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Felicitas Kutz
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Verena Linhard
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Tobias Matzel
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nathalie Meiser
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Niesteruk
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Dennis J. Pyper
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Linda Schulte
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Sven Trucks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Kamal Azzaoui
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Marcel J J Blommers
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Yojana Gadiya
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Drug Discovery Research ScreeningPort Screening Unit GERMANY
| | - Reagon Karki
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Marcius da Silva Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institue for Medical Biochemistry BRAZIL
| | - Cristiane Dinis Anobom
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Anna Lina Bula
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Institute of Organic Synthesis LATVIA
| | - Matthias Buetikofer
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute für Physikalische Chemie GERMANY
| | - Ícaro Putinhon Caruso
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics BRAZIL
| | - Isabella Caterina Felli
- University of Florence: Universita degli Studi di Firenze Magnetic Resonance Center (CERM) ITALY
| | - Andrea T Da Poian
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics GERMANY
| | - Gisele Cardoso de Amorim
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Multidisciplinary Center for Research in Biology BRAZIL
| | - Nikolaos K Fourkiotis
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Angelo Gallo
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Dhiman Ghosh
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | | | - Oksana Gorbatyuk
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Bing Hao
- UConn Health Department of Molecular Biology and Biopyhsics UNITED STATES
| | - Vilius Kurauskas
- UW Madison: University of Wisconsin Madison Department of Biochemistry UNITED STATES
| | - Lauriane Lecoq
- Universite de Lyon Molecular Microbiology and Structural Biochemistry FRANCE
| | - Yunfeng Li
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Nathane Cunha Mebus-Antunes
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Miguel Mompean
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Thais Cristtina Neves-Martins
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Marti Ninot-Pedrosa
- Universite Lyon 1 IUT Lyon 1 Molecular Microbiology and Structural Biochemistry FRANCE
| | - Anderson S Pinheiro
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Letizia Pontoriero
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Yulia Pustovalova
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Roland Riek
- ETH Zürich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | - Angus Robertson
- NIAMDD: National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | - Marie Jose Abi Saad
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Miguel A Treviño
- CSIC: Consejo Superior de Investigaciones Cientificas "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Aikaterini C Tsika
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Fabio C.L. Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Ad Bax
- National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | | | - Jeffrey C Hoch
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Kristaps Jaudzems
- Institute of Organic Synthesis of the Latvian Academy of Sciences: Latvijas Organiskas sintezes instituts Institute for Organic Chemistry LATVIA
| | - Douglas V Laurents
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Julien Orts
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Roberta Pieratelli
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Georgios A Spyroulias
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | | | - Jan Ferner
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Boris Fuertig
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Martin Hengesbach
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Frank Löhr
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nusrat Qureshi
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Christian Richter
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Krishna Saxena
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Andreas Schlundt
- Goethe-Universitat Frankfurt am Main Department for Biosciences GERMANY
| | - Sridhar Sreeramulu
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Wacker
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julia E Weigand
- TU Darmstadt: Technische Universitat Darmstadt Department of Biology GERMANY
| | | | - Jens Woehnert
- Goethe-Universitat Frankfurt am Main Department of Biological Sciences GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie Max-von-Laue-Str. 7 60438 Frankfurt GERMANY
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4
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Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso ÍP, Felli IC, Da Poian AT, de Amorim GC, Fourkiotis NK, Gallo A, Ghosh D, Gomes-Neto F, Gorbatyuk O, Hao B, Kurauskas V, Lecoq L, Li Y, Mebus-Antunes NC, Mompean M, Neves-Martins TC, Ninot-Pedrosa M, Pinheiro AS, Pontoriero L, Pustovalova Y, Riek R, Robertson A, Abi Saad MJ, Treviño MA, Tsika AC, Almeida FC, Bax A, Henzler-Wildman K, Hoch JC, Jaudzems K, Laurents DV, Orts J, Pieratelli R, Spyroulias GA, Duchardt-Ferner E, Ferner J, Fuertig B, Hengesbach M, Löhr F, Qureshi N, Richter C, Saxena K, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Woehnert J, Schwalbe H. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development. Angew Chem Int Ed Engl 2022; 61:e202205858. [PMID: 36115062 PMCID: PMC9539013 DOI: 10.1002/anie.202205858] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Indexed: 11/17/2022]
Abstract
SARS‐CoV‐2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti‐virals. Within the international Covid19‐NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80% of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR‐detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure‐based drug design against the SCoV2 proteome.
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Affiliation(s)
- Hannes Berg
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Nadide Altincekic
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Islam Alshamleh
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Jasleen Kaur Bains
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julius Blechar
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Betül Ceylan
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Vanessa de Jesus
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Christin Fuks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Santosh L. Gande
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Bruno Hargittay
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Marie T. Hutchinson
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Robin Krishnathas
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Felicitas Kutz
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Verena Linhard
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Tobias Matzel
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nathalie Meiser
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Niesteruk
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Dennis J. Pyper
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Linda Schulte
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Sven Trucks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Kamal Azzaoui
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Marcel J J Blommers
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Yojana Gadiya
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Drug Discovery Research ScreeningPort Screening Unit GERMANY
| | - Reagon Karki
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Marcius da Silva Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institue for Medical Biochemistry BRAZIL
| | - Cristiane Dinis Anobom
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Anna Lina Bula
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Institute of Organic Synthesis LATVIA
| | - Matthias Buetikofer
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute für Physikalische Chemie GERMANY
| | - Ícaro Putinhon Caruso
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics BRAZIL
| | - Isabella Caterina Felli
- University of Florence: Universita degli Studi di Firenze Magnetic Resonance Center (CERM) ITALY
| | - Andrea T Da Poian
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics GERMANY
| | - Gisele Cardoso de Amorim
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Multidisciplinary Center for Research in Biology BRAZIL
| | - Nikolaos K Fourkiotis
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Angelo Gallo
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Dhiman Ghosh
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | | | - Oksana Gorbatyuk
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Bing Hao
- UConn Health Department of Molecular Biology and Biopyhsics UNITED STATES
| | - Vilius Kurauskas
- UW Madison: University of Wisconsin Madison Department of Biochemistry UNITED STATES
| | - Lauriane Lecoq
- Universite de Lyon Molecular Microbiology and Structural Biochemistry FRANCE
| | - Yunfeng Li
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Nathane Cunha Mebus-Antunes
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Miguel Mompean
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Thais Cristtina Neves-Martins
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Marti Ninot-Pedrosa
- Universite Lyon 1 IUT Lyon 1 Molecular Microbiology and Structural Biochemistry FRANCE
| | - Anderson S Pinheiro
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Letizia Pontoriero
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Yulia Pustovalova
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Roland Riek
- ETH Zürich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | - Angus Robertson
- NIAMDD: National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | - Marie Jose Abi Saad
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Miguel A Treviño
- CSIC: Consejo Superior de Investigaciones Cientificas "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Aikaterini C Tsika
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Fabio C.L. Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Ad Bax
- National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | | | - Jeffrey C Hoch
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Kristaps Jaudzems
- Institute of Organic Synthesis of the Latvian Academy of Sciences: Latvijas Organiskas sintezes instituts Institute for Organic Chemistry LATVIA
| | - Douglas V Laurents
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Julien Orts
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Roberta Pieratelli
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Georgios A Spyroulias
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | | | - Jan Ferner
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Boris Fuertig
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Martin Hengesbach
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Frank Löhr
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nusrat Qureshi
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Christian Richter
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Krishna Saxena
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Andreas Schlundt
- Goethe-Universitat Frankfurt am Main Department for Biosciences GERMANY
| | - Sridhar Sreeramulu
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Wacker
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julia E Weigand
- TU Darmstadt: Technische Universitat Darmstadt Department of Biology GERMANY
| | | | - Jens Woehnert
- Goethe-Universitat Frankfurt am Main Department of Biological Sciences GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie Max-von-Laue-Str. 7 60438 Frankfurt GERMANY
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5
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Sreeramulu S, Richter C, Berg H, Wirtz Martin MA, Ceylan B, Matzel T, Adam J, Altincekic N, Azzaoui K, Bains JK, Blommers MJJ, Ferner J, Fürtig B, Göbel M, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Martins JN, Mertinkus KR, Niesteruk A, Peter SA, Pyper DJ, Qureshi NS, Scheffer U, Schlundt A, Schnieders R, Stirnal E, Sudakov A, Tröster A, Vögele J, Wacker A, Weigand JE, Wirmer‐Bartoschek J, Wöhnert J, Schwalbe H. Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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6
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Sreeramulu S, Richter C, Berg H, Wirtz Martin MA, Ceylan B, Matzel T, Adam J, Altincekic N, Azzaoui K, Bains JK, Blommers MJJ, Ferner J, Fürtig B, Göbel M, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Martins JN, Mertinkus KR, Niesteruk A, Peter SA, Pyper DJ, Qureshi NS, Scheffer U, Schlundt A, Schnieders R, Stirnal E, Sudakov A, Tröster A, Vögele J, Wacker A, Weigand JE, Wirmer‐Bartoschek J, Wöhnert J, Schwalbe H. Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS-CoV-2 Genome. Angew Chem Int Ed Engl 2021; 60:19191-19200. [PMID: 34161644 PMCID: PMC8426693 DOI: 10.1002/anie.202103693] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/03/2021] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 contains a positive single-stranded RNA genome of approximately 30 000 nucleotides. Within this genome, 15 RNA elements were identified as conserved between SARS-CoV and SARS-CoV-2. By nuclear magnetic resonance (NMR) spectroscopy, we previously determined that these elements fold independently, in line with data from in vivo and ex-vivo structural probing experiments. These elements contain non-base-paired regions that potentially harbor ligand-binding pockets. Here, we performed an NMR-based screening of a poised fragment library of 768 compounds for binding to these RNAs, employing three different 1 H-based 1D NMR binding assays. The screening identified common as well as RNA-element specific hits. The results allow selection of the most promising of the 15 RNA elements as putative drug targets. Based on the identified hits, we derive key functional units and groups in ligands for effective targeting of the RNA of SARS-CoV-2.
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7
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Greenidge PA, Blommers MJJ, Priestle JP, Hunziker J. How to Computationally Stack the Deck for Hit-to-Lead Generation: In Silico Molecular Interaction Energy Profiling for de Novo siRNA Guide Strand Surrogate Selection. J Chem Inf Model 2019; 59:1897-1908. [PMID: 31021613 DOI: 10.1021/acs.jcim.8b00892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The Argonaute-2 protein is part of the RNA-induced silencing complex (RISC) and anchors the guide strand of the small interfering RNA (siRNA). The 3'-end of the RNA contains two unpaired nucleotides (3'-overhang) that interact with the PAZ (PIWI/Argonaute/Zwille) domain of the protein. Theoretical and experimental evidence points toward a direct connection between the PAZ/3'-overhang binding affinity and siRNA's potency and specificity. Among the challenges to overcome when deploying siRNA molecules as therapeutics are their ready degradation under physiological conditions and off-target effects. It has been demonstrated that nuclease resistance can be improved via replacement of the dinucleotide overhang by small molecules which retain the interactions of the RNA guide strand with the PAZ domain. Most commonly, nucleotide analogues are used to substitute the siRNA overhang. However, in this study we adopt a de novo approach to its modification. The X-ray structure of human Argonaute-2 PAZ domain served to perform virtual screening and molecular interaction energy profiling (i.e., decomposition of the force field calculated protein-ligand interaction energies) of tailored-to-purpose fragment libraries. The binding of fragments to the PAZ domain was validated experimentally by NMR spectroscopy. The in silico guided protocol led to the efficient discovery of a number of PAZ domain ligands with affinities comparable to that of a reference dinucleotide (UpU, Kd = 33 μM). Originally starting from a generic fragment library, hits progress from 930 μM down to 14 μM within three iterations for the fragments selected via in silico molecular interaction energy profiling from a bespoke library. These dinucleotide siRNA guide strand surrogates represent potential new siRNA-based therapeutics (when attached to siRNA to form bioconjugates) featuring improved efficacy, specificity, stability, and cellular uptake. This project yielded a portfolio of seven patent applications, four of which have been granted to date.
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Affiliation(s)
- Paulette A Greenidge
- Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland.,Sprint Bioscience AB , Hälsovägen 7 , SE-141 57 Huddinge , Sweden
| | - Marcel J J Blommers
- Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland.,Saverna Therapeutics AG , Pumpmattenweg 3 , CH-4105 Biel-Benken , Switzerland
| | - John P Priestle
- Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland
| | - Jürg Hunziker
- Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland
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8
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Palacino J, Swalley SE, Song C, Cheung AK, Shu L, Zhang X, Van Hoosear M, Shin Y, Chin DN, Keller CG, Beibel M, Renaud NA, Smith TM, Salcius M, Shi X, Hild M, Servais R, Jain M, Deng L, Bullock C, McLellan M, Schuierer S, Murphy L, Blommers MJJ, Blaustein C, Berenshteyn F, Lacoste A, Thomas JR, Roma G, Michaud GA, Tseng BS, Porter JA, Myer VE, Tallarico JA, Hamann LG, Curtis D, Fishman MC, Dietrich WF, Dales NA, Sivasankaran R. Corrigendum: SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice. Nat Chem Biol 2016; 12:304. [PMID: 26991088 DOI: 10.1038/nchembio0416-304c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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9
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Palacino J, Swalley SE, Song C, Cheung AK, Shu L, Zhang X, Van Hoosear M, Shin Y, Chin DN, Keller CG, Beibel M, Renaud NA, Smith TM, Salcius M, Shi X, Hild M, Servais R, Jain M, Deng L, Bullock C, McLellan M, Schuierer S, Murphy L, Blommers MJJ, Blaustein C, Berenshteyn F, Lacoste A, Thomas JR, Roma G, Michaud GA, Tseng BS, Porter JA, Myer VE, Tallarico JA, Hamann LG, Curtis D, Fishman MC, Dietrich WF, Dales NA, Sivasankaran R. Erratum: Corrigendum: SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice. Nat Chem Biol 2015; 11:741. [DOI: 10.1038/nchembio0915-741a] [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: 11/09/2022]
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10
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Palacino J, Swalley SE, Song C, Cheung AK, Shu L, Zhang X, Van Hoosear M, Shin Y, Chin DN, Keller CG, Beibel M, Renaud NA, Smith TM, Salcius M, Shi X, Hild M, Servais R, Jain M, Deng L, Bullock C, McLellan M, Schuierer S, Murphy L, Blommers MJJ, Blaustein C, Berenshteyn F, Lacoste A, Thomas JR, Roma G, Michaud GA, Tseng BS, Porter JA, Myer VE, Tallarico JA, Hamann LG, Curtis D, Fishman MC, Dietrich WF, Dales NA, Sivasankaran R. SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice. Nat Chem Biol 2015; 11:511-7. [PMID: 26030728 DOI: 10.1038/nchembio.1837] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 05/06/2015] [Indexed: 12/17/2022]
Abstract
Spinal muscular atrophy (SMA), which results from the loss of expression of the survival of motor neuron-1 (SMN1) gene, represents the most common genetic cause of pediatric mortality. A duplicate copy (SMN2) is inefficiently spliced, producing a truncated and unstable protein. We describe herein a potent, orally active, small-molecule enhancer of SMN2 splicing that elevates full-length SMN protein and extends survival in a severe SMA mouse model. We demonstrate that the molecular mechanism of action is via stabilization of the transient double-strand RNA structure formed by the SMN2 pre-mRNA and U1 small nuclear ribonucleic protein (snRNP) complex. The binding affinity of U1 snRNP to the 5' splice site is increased in a sequence-selective manner, discrete from constitutive recognition. This new mechanism demonstrates the feasibility of small molecule-mediated, sequence-selective splice modulation and the potential for leveraging this strategy in other splicing diseases.
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Affiliation(s)
- James Palacino
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Susanne E Swalley
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Cheng Song
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Atwood K Cheung
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Lei Shu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Xiaolu Zhang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Mailin Van Hoosear
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Youngah Shin
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Donovan N Chin
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | | | - Martin Beibel
- Novartis Institutes for Biomedical Research, Forum 1, Basel, Switzerland
| | - Nicole A Renaud
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Thomas M Smith
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Michael Salcius
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Xiaoying Shi
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Marc Hild
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Rebecca Servais
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Monish Jain
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Lin Deng
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Caroline Bullock
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Michael McLellan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Sven Schuierer
- Novartis Institutes for Biomedical Research, Forum 1, Basel, Switzerland
| | - Leo Murphy
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | | | - Cecile Blaustein
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Frada Berenshteyn
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Arnaud Lacoste
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jason R Thomas
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Forum 1, Basel, Switzerland
| | - Gregory A Michaud
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Brian S Tseng
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jeffery A Porter
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Vic E Myer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - John A Tallarico
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Lawrence G Hamann
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Daniel Curtis
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Mark C Fishman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - William F Dietrich
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Natalie A Dales
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
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11
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Brachmann SM, Kleylein-Sohn J, Gaulis S, Kauffmann A, Blommers MJJ, Kazic-Legueux M, Laborde L, Hattenberger M, Stauffer F, Vaxelaire J, Romanet V, Henry C, Murakami M, Guthy DA, Sterker D, Bergling S, Wilson C, Brümmendorf T, Fritsch C, Garcia-Echeverria C, Sellers WR, Hofmann F, Maira SM. Characterization of the mechanism of action of the pan class I PI3K inhibitor NVP-BKM120 across a broad range of concentrations. Mol Cancer Ther 2012; 11:1747-57. [PMID: 22653967 DOI: 10.1158/1535-7163.mct-11-1021] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The pan-phosphoinositide 3-kinase (PI3K) inhibitor BKM120 was found, at high concentrations, to cause cell death in various cellular systems, irrespective of their level of PI3K addiction. Transcriptional and biochemical profiling studies were used to identify the origin of these unexpected and apparently PI3K-independent effects. At 5- to 10-fold, the concentration needed to half-maximally inhibit PI3K signaling. BKM120 treatment caused changes in expression of mitotic genes and the induction of a robust G(2)-M arrest. Tubulin polymerization assays and nuclear magnetic resonance-binding studies revealed that BKM120 inhibited microtubule dynamics upon direct binding to tubulin. To assess the contribution of this off-target activity vis-à-vis the antitumor activity of BKM120 in PI3K-dependent tumors, we used a mechanistic PI3K-α-dependent model. We observed that, in vivo, daily treatment of mice with doses of BKM120 up to 40 mg/kg led to tumor regressions with no increase in the mitotic index. Thus, strong antitumor activity can be achieved in PI3K-dependent models at exposures that are below those necessary to engage the off-target activity. In comparison, the clinical data indicate that it is unlikely that BKM120 will achieve exposures sufficient to significantly engage the off-target activity at tolerated doses and schedules. However, in preclinical settings, the consequences of the off-target activity start to manifest themselves at concentrations above 1 μmol/L in vitro and doses above 50 mg/kg in efficacy studies using subcutaneous tumor-bearing mice. Hence, careful concentration and dose range selection is required to ensure that any observation can be correctly attributed to BKM120 inhibition of PI3K.
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Affiliation(s)
- Saskia M Brachmann
- NIBR Oncology Disease Area, Novartis Pharma AG, Basel CH4002, Switzerland.
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12
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Petrovskaya LE, Shulga AA, Bocharova OV, Ermolyuk YS, Kryukova EA, Chupin VV, Blommers MJJ, Arseniev AS, Kirpichnikov MP. Expression of G-protein coupled receptors in Escherichia coli for structural studies. Biochemistry (Mosc) 2010; 75:881-91. [PMID: 20673212 DOI: 10.1134/s0006297910070102] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
To elaborate a high-performance system for expression of genes of G-protein coupled receptors (GPCR), methods of direct and hybrid expression of 17 GPCR genes in Escherichia coli and selection of strains and bacteria cultivation conditions were investigated. It was established that expression of most of the target GPCR fused with the N-terminal fragment of OmpF or Mistic using media for autoinduction provides high output (up to 50 mg/liter).
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Affiliation(s)
- L E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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13
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Kumar A, Heise H, Blommers MJJ, Krastel P, Schmitt E, Petersen F, Jeganathan S, Mandelkow EM, Carlomagno T, Griesinger C, Baldus M. Interaction of Epothilone B (Patupilone) with Microtubules as Detected by Two-Dimensional Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001946] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Kumar A, Heise H, Blommers MJJ, Krastel P, Schmitt E, Petersen F, Jeganathan S, Mandelkow EM, Carlomagno T, Griesinger C, Baldus M. Interaction of Epothilone B (Patupilone) with Microtubules as Detected by Two-Dimensional Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2010; 49:7504-7. [DOI: 10.1002/anie.201001946] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Shenkarev ZO, Paramonov AS, Lyukmanova EN, Shingarova LN, Yakimov SA, Dubinnyi MA, Chupin VV, Kirpichnikov MP, Blommers MJJ, Arseniev AS. NMR structural and dynamical investigation of the isolated voltage-sensing domain of the potassium channel KvAP: implications for voltage gating. J Am Chem Soc 2010; 132:5630-7. [PMID: 20356312 DOI: 10.1021/ja909752r] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure and dynamics of the isolated voltage-sensing domain (VSD) of the archaeal potassium channel KvAP was studied by high-resolution NMR. The almost complete backbone resonance assignment and partial side-chain assignment of the (2)H,(13)C,(15)N-labeled VSD were obtained for the protein domain solubilized in DPC/LDAO (2:1) mixed micelles. Secondary and tertiary structures of the VSD were characterized using secondary chemical shifts and NOE contacts. These data indicate that the spatial structure of the VSD solubilized in micelles corresponds to the structure of the domain in an open state of the channel. NOE contacts and secondary chemical shifts of amide protons indicate the presence of tightly bound water molecule as well as hydrogen bond formation involving an interhelical salt bridge (Asp62-R133) that stabilizes the overall structure of the domain. The backbone dynamics of the VSD was studied using (15)N relaxation measurements. The loop regions S1-S2 and S2-S3 were found mobile, while the S3-S4 loop (voltage-sensor paddle) was found stable at the ps-ns time scale. The moieties of S1, S2, S3, and S4 helices sharing interhelical contacts (at the level of the Asp62-R133 salt bridge) were observed in conformational exchange on the micros-ms time scale. Similar exchange-induced broadening of characteristic resonances was observed for the VSD solubilized in the membrane of lipid-protein nanodiscs composed of DMPC, DMPG, and POPC/DOPG lipids. Apparently, the observed interhelical motions represent an inherent property of the VSD of the KvAP channel and can play an important role in the voltage gating.
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Affiliation(s)
- Zakhar O Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia.
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16
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Shenkarev ZO, Lyukmanova EN, Paramonov AS, Shingarova LN, Chupin VV, Kirpichnikov MP, Blommers MJJ, Arseniev AS. Lipid−Protein Nanodiscs as Reference Medium in Detergent Screening for High-Resolution NMR Studies of Integral Membrane Proteins. J Am Chem Soc 2010; 132:5628-9. [DOI: 10.1021/ja9097498] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zakhar O. Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Ekaterina N. Lyukmanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Alexander S. Paramonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Lyudmila N. Shingarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Vladimir V. Chupin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Marcel J. J. Blommers
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Alexander S. Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., 117997 Moscow, Russia and Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
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Gossert AD, Henry C, Blommers MJJ, Jahnke W, Fernández C. Time efficient detection of protein-ligand interactions with the polarization optimized PO-WaterLOGSY NMR experiment. J Biomol NMR 2009; 43:211-217. [PMID: 19205897 DOI: 10.1007/s10858-009-9303-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 01/16/2009] [Indexed: 05/27/2023]
Abstract
The identification of compounds that bind to a protein of interest is of central importance in contemporary drug research. For screening of compound libraries, NMR techniques are widely used, in particular the Water-Ligand Observed via Gradient SpectroscopY (WaterLOGSY) experiment. Here we present an optimized experiment, the polarization optimized WaterLOGSY (PO-WaterLOGSY). Based on a water flip-back strategy in conjunction with model calculations and numerical simulations, the PO-WaterLOGSY is optimized for water polarization recovery. Compared to a standard setup with the conventional WaterLOGSY, time consuming relaxation delays have been considerably shortened and can even be omitted through this approach. Furthermore, the robustness of the pulse sequence in an industrial setup was increased by the use of hard pulse trains for selective water excitation and water suppression. The PO-WaterLOGSY thus yields increased time efficiency by factor of 3-5 when compared with previously published schemes. These time savings have a substantial impact in drug discovery, since significantly larger compound libraries can be tested in screening campaigns.
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Affiliation(s)
- Alvar D Gossert
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002, Basel, Switzerland
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18
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Lyukmanova EN, Shenkarev ZO, Paramonov AS, Sobol AG, Ovchinnikova TV, Chupin VV, Kirpichnikov MP, Blommers MJJ, Arseniev AS. Lipid−Protein Nanoscale Bilayers: A Versatile Medium for NMR Investigations of Membrane Proteins and Membrane-Active Peptides. J Am Chem Soc 2008; 130:2140-1. [DOI: 10.1021/ja0777988] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Kallen J, Lattmann R, Beerli R, Blechschmidt A, Blommers MJJ, Geiser M, Ottl J, Schlaeppi JM, Strauss A, Fournier B. Crystal structure of human estrogen-related receptor alpha in complex with a synthetic inverse agonist reveals its novel molecular mechanism. J Biol Chem 2007; 282:23231-9. [PMID: 17556356 DOI: 10.1074/jbc.m703337200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Inverse agonists of the constitutively active human estrogen-related receptor alpha (ERRalpha, NR3B1) are of potential interest for several disease indications (e.g. breast cancer, metabolic diseases, or osteoporosis). ERRalpha is constitutively active, because its ligand binding pocket (LBP) is practically filled with side chains (in particular with Phe(328), which is replaced by Ala in ERRbeta and ERRgamma). We present here the crystal structure of the ligand binding domain of ERRalpha (containing the mutation C325S) in complex with the inverse agonist cyclohexylmethyl-(1-p-tolyl-1H-indol-3-ylmethyl)-amine (compound 1a), to a resolution of 2.3A(.) The structure reveals the dramatic multiple conformational changes in the LBP, which create the necessary space for the ligand. As a consequence of the new side chain conformation of Phe(328) (on helix H3), Phe(510)(H12) has to move away, and thus the activation helix H12 is displaced from its agonist position. This is a novel mechanism of H12 inactivation, different from ERRgamma, estrogen receptor (ER) alpha, and ERbeta. H12 binds (with a surprising binding mode) in the coactivator groove of its ligand binding domain, at a similar place as a coactivator peptide. This is in contrast to ERRgamma but resembles the situation for ERalpha (raloxifene or 4-hydroxytamoxifen complexes). Our results explain the novel molecular mechanism of an inverse agonist for ERRalpha and provide the basis for rational drug design to obtain isotype-specific inverse agonists of this potential new drug target. Despite a practically filled LBP, the finding that a suitable ligand can induce an opening of the cavity also has broad implications for other orphan nuclear hormone receptors (e.g. the NGFI-B subfamily).
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Affiliation(s)
- Joerg Kallen
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland.
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20
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Reese M, Sánchez-Pedregal VM, Kubicek K, Meiler J, Blommers MJJ, Griesinger C, Carlomagno T. Structural basis of the activity of the microtubule-stabilizing agent epothilone a studied by NMR spectroscopy in solution. Angew Chem Int Ed Engl 2007; 46:1864-8. [PMID: 17274084 DOI: 10.1002/anie.200604505] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marcel Reese
- Abteilung für NMR-basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany
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21
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Sánchez-Pedregal VM, Reese M, Meiler J, Blommers MJJ, Griesinger C, Carlomagno T. The INPHARMA method: protein-mediated interligand NOEs for pharmacophore mapping. Angew Chem Int Ed Engl 2006; 44:4172-5. [PMID: 15929149 DOI: 10.1002/anie.200500503] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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22
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Jahnke W, Blommers MJJ, Fernández C, Zwingelstein C, Amstutz R. Strategies for the NMR-based identification and optimization of allosteric protein kinase inhibitors. Chembiochem 2006; 6:1607-10. [PMID: 16028302 DOI: 10.1002/cbic.200500100] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Discovery Technologies, WSJ-88.904, 4002 Basel, Switzerland.
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23
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Sánchez-Pedregal VM, Reese M, Meiler J, Blommers MJJ, Griesinger C, Carlomagno T. The INPHARMA Method: Protein-Mediated Interligand NOEs for Pharmacophore Mapping. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500503] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [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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24
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Carlomagno T, Blommers MJJ, Meiler J, Jahnke W, Schupp T, Petersen F, Schinzer D, Altmann KH, Griesinger C. The high-resolution solution structure of epothilone A bound to tubulin: an understanding of the structure-activity relationships for a powerful class of antitumor agents. Angew Chem Int Ed Engl 2003; 42:2511-5. [PMID: 12800173 DOI: 10.1002/anie.200351276] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Teresa Carlomagno
- Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37 077 Göttingen, Germany.
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Carlomagno T, Sánchez VM, Blommers MJJ, Griesinger C. Derivation of dihedral angles from CH-CH dipolar-dipolar cross-correlated relaxation rates: a C-C torsion involving a quaternary carbon atom in epothilone A bound to tubulin. Angew Chem Int Ed Engl 2003; 42:2515-7. [PMID: 12800174 DOI: 10.1002/anie.200350950] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Teresa Carlomagno
- Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany.
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26
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Carlomagno T, Blommers MJJ, Meiler J, Jahnke W, Schupp T, Petersen F, Schinzer D, Altmann KH, Griesinger C. Cover Picture: The High-Resolution Solution Structure of Epothilone A Bound to Tubulin: An Understanding of the Structure–Activity Relationships for a Powerful Class of Antitumor Agents (Angew. Chem. Int. Ed. 22/2003). Angew Chem Int Ed Engl 2003. [DOI: 10.1002/anie.200390473] [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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Carlomagno T, Blommers MJJ, Meiler J, Jahnke W, Schupp T, Petersen F, Schinzer D, Altmann K, Griesinger C. Angew Chem Int Ed Engl 2003; 115:2615-2619. [DOI: 10.1002/ange.200351276] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Carlomagno T, Blommers MJJ, Meiler J, Jahnke W, Schupp T, Petersen F, Schinzer D, Altmann KH, Griesinger C. Titelbild: The High-Resolution Solution Structure of Epothilone A Bound to Tubulin: An Understanding of the Structure–Activity Relationships for a Powerful Class of Antitumor Agents (Angew. Chem. 22/2003). Angew Chem Int Ed Engl 2003. [DOI: 10.1002/ange.200390500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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30
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Abstract
One of the prime merits of NMR as a tool for lead finding in drug discovery research is its sensitivity and robustness to detect weak protein-ligand interactions. This sensitivity allows to build up ligands for a given target in a modular way, by a fragment-based approach. In this approach, two ligands are seperately identified which bind to the target protein generally weakly, but at adjacent binding sites. In a next step, they are chemically linked to produce a high-affinity ligand. This review discusses methods to detect "second-site" ligands that bind to a protein in the presence of a "first-site" ligand, and methods to elucidate structural details on the spatial orientation of both ligands, so that chemical linkage is based on a large piece of experimental information. Published examples from second-site screening and linker design are summarized, and are complemented by previously unpublished in-house examples.
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Affiliation(s)
- Wolfgang Jahnke
- Novartis Pharma AG, Central Technologies and Oncology Research, CH-4002 Basel, Switzerland.
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31
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Abstract
There are conceptual differences between high-throughput screening (HTS) and fragment-based screening by NMR. The number of compounds in libraries for NMR screening may be significantly smaller than those used for HTS. Because one relies on a small library its design is significantly important and is the object of this article. A short introduction on fragment-based NMR screening approaches will be provided. Although there are currently very few reports describing the design of libraries of small molecules for NMR screening, aspects of the question of how to compile diverse collections of small molecular fragments useful for drug design were previously addressed for the purposes of combinatorial library design and de novo drug design. As these disciplines are highly interrelated and are applied in an interconnected manner with NMR screening within the drug discovery process, a review of combinatorial library design and especially the building block or fragment selection strategies applied for combinatorial library design and de novo design is well suited to reveal fundamental strategies and potential techniques for the design of NMR screening libraries. This section will be rounded off by a report on hands-on-experience with the design of the Novartis second-site NMR screening library and practical considerations for the design of compound mixtures. Rather than providing an exact protocol general guidelines will be indicated.
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Affiliation(s)
- Edgar Jacoby
- Novartis Pharma AG, Drug Discovery Center, Compound Management and Computation Unit, CH-4002 Basel, Switzerland.
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Bocharov EV, Korzhnev DM, Blommers MJJ, Arvinte T, Orekhov VY, Billeter M, Arseniev AS. Dynamics-modulated biological activity of transforming growth factor beta3. J Biol Chem 2002; 277:46273-9. [PMID: 12221089 DOI: 10.1074/jbc.m206274200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transforming growth factor beta3 (TGF-beta3) is an important mediator of growth, maintenance, and repair processes in human cells. Internal dynamic properties have been derived from (15)N NMR relaxation data and mapped onto the spatial structure of TGF-beta3. The pattern of internal dynamics in the structure identifies potential "hot spots" of binding free energy and reveals the importance of conformational entropy in the interaction of TGF-beta3 with the receptors. The observed internal dynamics set TGF-beta3 apart from other TGF-beta isoforms, with which it shares the same fold. These findings may explain functional differences among the various TGF-beta isoforms and thus prove essential in the search for related therapeutic agents.
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Affiliation(s)
- Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997, Russia
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Blommers MJJ, Stark W, Jones CE, Head D, Owen CE, Jahnke W. Transferred Cross-Correlated Relaxation Complements Transferred NOE: Structure of an IL-4R-Derived Peptide Bound to STAT-6. J Am Chem Soc 1999. [DOI: 10.1021/ja9836545] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcel J. J. Blommers
- Contribution from Core Technologies, Novartis Pharma AG, P.O. Box, CH-4002 Basel, Switzerland, and Molecular and Cell Biology Unit, Novartis Horsham Research Centre, Wimblehurst Road, Horsham, West Sussex, RH12 5AB, United Kingdom
| | - Wilhelm Stark
- Contribution from Core Technologies, Novartis Pharma AG, P.O. Box, CH-4002 Basel, Switzerland, and Molecular and Cell Biology Unit, Novartis Horsham Research Centre, Wimblehurst Road, Horsham, West Sussex, RH12 5AB, United Kingdom
| | - Carol E. Jones
- Contribution from Core Technologies, Novartis Pharma AG, P.O. Box, CH-4002 Basel, Switzerland, and Molecular and Cell Biology Unit, Novartis Horsham Research Centre, Wimblehurst Road, Horsham, West Sussex, RH12 5AB, United Kingdom
| | - Denis Head
- Contribution from Core Technologies, Novartis Pharma AG, P.O. Box, CH-4002 Basel, Switzerland, and Molecular and Cell Biology Unit, Novartis Horsham Research Centre, Wimblehurst Road, Horsham, West Sussex, RH12 5AB, United Kingdom
| | - Charles E. Owen
- Contribution from Core Technologies, Novartis Pharma AG, P.O. Box, CH-4002 Basel, Switzerland, and Molecular and Cell Biology Unit, Novartis Horsham Research Centre, Wimblehurst Road, Horsham, West Sussex, RH12 5AB, United Kingdom
| | - Wolfgang Jahnke
- Contribution from Core Technologies, Novartis Pharma AG, P.O. Box, CH-4002 Basel, Switzerland, and Molecular and Cell Biology Unit, Novartis Horsham Research Centre, Wimblehurst Road, Horsham, West Sussex, RH12 5AB, United Kingdom
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Jahnke W, Kolb HC, Blommers MJJ, Magnani JL, Ernst B. Comparison of the Bioactive Conformations of Sialyl LewisX and a Potent Sialyl LewisX Mimic. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/anie.199726031] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Jahnke W, Kolb HC, Blommers MJJ, Ernst B, Magnani JL. Vergleich der bioaktiven Konformationen von Sialyl-LewisX und einem potenten Sialyl-LewisX-Mimetikum. Angew Chem Int Ed Engl 1997. [DOI: 10.1002/ange.19971092310] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Earnest I, Kalvoda J, Francotte E, Rihs G, Fritz H, Blommers MJJ, Raschdorf F, Sigel C, Mutter M. Template-Assembled Synthetic Proteins (TASP). Cyclic Templates with Incorporated Turn-Inducing Mimics. Helv Chim Acta 1993. [DOI: 10.1002/hlca.19930760414] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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