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Lima GMA, Jagudin E, Talibov VO, Benz LS, Marullo C, Barthel T, Wollenhaupt J, Weiss MS, Mueller U. FragMAXapp: crystallographic fragment-screening data-analysis and project-management system. Acta Crystallogr D Struct Biol 2021; 77:799-808. [PMID: 34076593 PMCID: PMC8171072 DOI: 10.1107/s2059798321003818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 09/25/2020] [Accepted: 04/08/2021] [Indexed: 01/13/2023] Open
Abstract
Crystallographic fragment screening (CFS) has become one of the major techniques for screening compounds in the early stages of drug-discovery projects. Following the advances in automation and throughput at modern macromolecular crystallography beamlines, the bottleneck for CFS has shifted from collecting data to organizing and handling the analysis of such projects. The complexity that emerges from the use of multiple methods for processing and refinement and to search for ligands requires an equally sophisticated solution to summarize the output, allowing researchers to focus on the scientific questions instead of on software technicalities. FragMAXapp is the fragment-screening project-management tool designed to handle CFS projects at MAX IV Laboratory. It benefits from the powerful computing infrastructure of large-scale facilities and, as a web application, it is accessible from everywhere.
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Affiliation(s)
| | - Elmir Jagudin
- BioMAX, MAX IV Laboratory, Fotongatan 2, 224 84 Lund, Sweden
| | | | - Laila S. Benz
- Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | | | - Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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Wollenhaupt J, Barthel T, Lima GMA, Metz A, Wallacher D, Jagudin E, Huschmann FU, Hauß T, Feiler CG, Gerlach M, Hellmig M, Förster R, Steffien M, Heine A, Klebe G, Mueller U, Weiss MS. Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin. J Vis Exp 2021. [PMID: 33749678 DOI: 10.3791/62208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Fragment screening is a technique that helps to identify promising starting points for ligand design. Given that crystals of the target protein are available and display reproducibly high-resolution X-ray diffraction properties, crystallography is among the most preferred methods for fragment screening because of its sensitivity. Additionally, it is the only method providing detailed 3D information of the binding mode of the fragment, which is vital for subsequent rational compound evolution. The routine use of the method depends on the availability of suitable fragment libraries, dedicated means to handle large numbers of samples, state-of-the-art synchrotron beamlines for fast diffraction measurements and largely automated solutions for the analysis of the results. Here, the complete practical workflow and the included tools on how to conduct crystallographic fragment screening (CFS) at the Helmholtz-Zentrum Berlin (HZB) are presented. Preceding this workflow, crystal soaking conditions as well as data collection strategies are optimized for reproducible crystallographic experiments. Then, typically in a one to two-day procedure, a 96-membered CFS-focused library provided as dried ready-to-use plates is employed to soak 192 crystals, which are then flash-cooled individually. The final diffraction experiments can be performed within one day at the robot-mounting supported beamlines BL14.1 and BL14.2 at the BESSY II electron storage ring operated by the HZB in Berlin-Adlershof (Germany). Processing of the crystallographic data, refinement of the protein structures, and hit identification is fast and largely automated using specialized software pipelines on dedicated servers, requiring little user input. Using the CFS workflow at the HZB enables routine screening experiments. It increases the chances for successful identification of fragment hits as starting points to develop more potent binders, useful for pharmacological or biochemical applications.
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Affiliation(s)
| | - Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin; Structural Biochemistry Group, Institute for Chemistry and Biochemistry, Freie Universität Berlin
| | | | - Alexander Metz
- Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg
| | | | | | - Franziska U Huschmann
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin; Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg
| | - Thomas Hauß
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin
| | | | - Martin Gerlach
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin
| | | | - Ronald Förster
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin
| | | | - Andreas Heine
- Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg
| | - Gerhard Klebe
- Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg
| | - Uwe Mueller
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin
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Ursby T, Åhnberg K, Appio R, Aurelius O, Barczyk A, Bartalesi A, Bjelčić M, Bolmsten F, Cerenius Y, Doak RB, Eguiraun M, Eriksson T, Friel RJ, Gorgisyan I, Gross A, Haghighat V, Hennies F, Jagudin E, Norsk Jensen B, Jeppsson T, Kloos M, Lidon-Simon J, de Lima GMA, Lizatovic R, Lundin M, Milan-Otero A, Milas M, Nan J, Nardella A, Rosborg A, Shilova A, Shoeman RL, Siewert F, Sondhauss P, Talibov VO, Tarawneh H, Thånell J, Thunnissen M, Unge J, Ward C, Gonzalez A, Mueller U. BioMAX - the first macromolecular crystallography beamline at MAX IV Laboratory. J Synchrotron Radiat 2020; 27:1415-1429. [PMID: 32876619 PMCID: PMC7467343 DOI: 10.1107/s1600577520008723] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/28/2020] [Indexed: 05/12/2023]
Abstract
BioMAX is the first macromolecular crystallography beamline at the MAX IV Laboratory 3 GeV storage ring, which is the first operational multi-bend achromat storage ring. Due to the low-emittance storage ring, BioMAX has a parallel, high-intensity X-ray beam, even when focused down to 20 µm × 5 µm using the bendable focusing mirrors. The beam is tunable in the energy range 5-25 keV using the in-vacuum undulator and the horizontally deflecting double-crystal monochromator. BioMAX is equipped with an MD3 diffractometer, an ISARA high-capacity sample changer and an EIGER 16M hybrid pixel detector. Data collection at BioMAX is controlled using the newly developed MXCuBE3 graphical user interface, and sample tracking is handled by ISPyB. The computing infrastructure includes data storage and processing both at MAX IV and the Lund University supercomputing center LUNARC. With state-of-the-art instrumentation, a high degree of automation, a user-friendly control system interface and remote operation, BioMAX provides an excellent facility for most macromolecular crystallography experiments. Serial crystallography using either a high-viscosity extruder injector or the MD3 as a fixed-target scanner is already implemented. The serial crystallography activities at MAX IV Laboratory will be further developed at the microfocus beamline MicroMAX, when it comes into operation in 2022. MicroMAX will have a 1 µm × 1 µm beam focus and a flux up to 1015 photons s-1 with main applications in serial crystallography, room-temperature structure determinations and time-resolved experiments.
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Affiliation(s)
- Thomas Ursby
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Karl Åhnberg
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Roberto Appio
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Oskar Aurelius
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Artur Barczyk
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Antonio Bartalesi
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Monika Bjelčić
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Fredrik Bolmsten
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Yngve Cerenius
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - R. Bruce Doak
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Mikel Eguiraun
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Thomas Eriksson
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Ross J. Friel
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Ishkhan Gorgisyan
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Andrea Gross
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Vahid Haghighat
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Franz Hennies
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Elmir Jagudin
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | | | - Tobias Jeppsson
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Marco Kloos
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Julio Lidon-Simon
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | | | - Robert Lizatovic
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Magnus Lundin
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | | | - Mirko Milas
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Jie Nan
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Alberto Nardella
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Anders Rosborg
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Anastasya Shilova
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Robert L. Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Frank Siewert
- Helmholtz Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany
| | - Peter Sondhauss
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | | | - Hamed Tarawneh
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Johan Thånell
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | | | - Johan Unge
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Christopher Ward
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Ana Gonzalez
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
| | - Uwe Mueller
- MAX IV Laboratory, Lund University, PO Box 118, S-221 00 Lund, Sweden
- Helmholtz Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany
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Lima GMA, Talibov VO, Jagudin E, Sele C, Nyblom M, Knecht W, Logan DT, Sjögren T, Mueller U. FragMAX: the fragment-screening platform at the MAX IV Laboratory. Acta Crystallogr D Struct Biol 2020; 76:771-777. [PMID: 32744259 PMCID: PMC7397489 DOI: 10.1107/s205979832000889x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 04/26/2020] [Accepted: 06/30/2020] [Indexed: 01/06/2023] Open
Abstract
Advances in synchrotron storage rings and beamline automation have pushed data-collection rates to thousands of data sets per week. With this increase in throughput, massive projects such as in-crystal fragment screening have become accessible to a larger number of research groups. The quality of support offered at large-scale facilities allows medicinal chemistry-focused or biochemistry-focused groups to supplement their research with structural biology. Preparing the experiment, analysing multiple data sets and prospecting for interesting complexes of protein and fragments require, for both newcomers and experienced users, efficient management of the project and extensive computational power for data processing and structure refinement. Here, FragMAX, a new complete platform for fragment screening at the BioMAX beamline of the MAX IV Laboratory, is described. The ways in which users are assisted in X-ray-based fragment screenings and in which the fourth-generation storage ring available at the facility is best exploited are also described.
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Affiliation(s)
| | | | - Elmir Jagudin
- BioMAX, MAX IV Laboratory, Fotongatan 2, 224 84 Lund, Sweden
| | - Céleste Sele
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden
| | - Maria Nyblom
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden
| | - Wolfgang Knecht
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden
| | - Derek T. Logan
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, Box 124, 221 00 Lund, Sweden
- SARomics Biostructures AB, Medicon Village, Scheeletorget 1, 223 63 Lund, Sweden
| | - Tove Sjögren
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Uwe Mueller
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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