1
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Mukherjee M, Day PJ, Laverty D, Bueren-Calabuig JA, Woodhead AJ, Griffiths-Jones C, Hiscock S, East C, Boyd S, O'Reilly M. Protein engineering enables a soakable crystal form of human CDK7 primed for high-throughput crystallography and structure-based drug design. Structure 2024:S0969-2126(24)00188-6. [PMID: 38870939 DOI: 10.1016/j.str.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/08/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Cyclin dependent kinase 7 (CDK7) is an important therapeutic kinase best known for its dual role in cell cycle regulation and gene transcription. Here, we describe the application of protein engineering to generate constructs leading to high resolution crystal structures of human CDK7 in both active and inactive conformations. The active state of the kinase was crystallized by incorporation of an additional surface residue mutation (W132R) onto the double phosphomimetic mutant background (S164D and T170E) that yielded the inactive kinase structure. A novel back-soaking approach was developed to determine crystal structures of several clinical and pre-clinical inhibitors of this kinase, demonstrating the potential utility of the crystal system for structure-based drug design (SBDD). The crystal structures help to rationalize the mode of inhibition and the ligand selectivity profiles versus key anti-targets. The protein engineering approach described here illustrates a generally applicable strategy for structural enablement of challenging molecular targets.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Susan Boyd
- Astex Pharmaceuticals, Cambridge CB4 0QA, UK
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2
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Füsser FT, Wollenhaupt J, Weiss MS, Kümmel D, Koch O. Novel starting points for fragment-based drug design against mycobacterial thioredoxin reductase identified using crystallographic fragment screening. Acta Crystallogr D Struct Biol 2023; 79:857-865. [PMID: 37574972 PMCID: PMC10478635 DOI: 10.1107/s2059798323005223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/12/2023] [Indexed: 08/15/2023] Open
Abstract
The increasing number of people dying from tuberculosis and the existence of extensively drug-resistant strains has led to an urgent need for new antituberculotic drugs with alternative modes of action. As part of the thioredoxin system, thioredoxin reductase (TrxR) is essential for the survival of Mycobacterium tuberculosis (Mtb) and shows substantial differences from human TrxR, making it a promising and most likely selective target. As a model organism for Mtb, crystals of Mycobacterium smegmatis TrxR that diffracted to high resolution were used in crystallographic fragment screening to discover binding fragments and new binding sites. The application of the 96 structurally diverse fragments from the F2X-Entry Screen revealed 56 new starting points for fragment-based drug design of new TrxR inhibitors. Over 200 crystal structures were analyzed using FragMAXapp, which includes processing and refinement by largely automated software pipelines and hit identification via the multi-data-set analysis approach PanDDA. The fragments are bound to 11 binding sites, of which four are positioned at binding pockets or important interaction sites and therefore show high potential for possible inhibition of TrxR.
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Affiliation(s)
- Friederike T. Füsser
- Institute of Pharmaceutical and Medicinal Chemistry, Münster University, Corrensstrasse 48, 48149 Münster, Germany
- German Center of Infection Research, Münster University, Corrensstrasse 48, 48149 Münster, Germany
- Institute of Biochemistry, Münster University, Corrensstrasse 36, 48149 Münster, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography Group, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography Group, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Daniel Kümmel
- Institute of Biochemistry, Münster University, Corrensstrasse 36, 48149 Münster, Germany
| | - Oliver Koch
- Institute of Pharmaceutical and Medicinal Chemistry, Münster University, Corrensstrasse 48, 48149 Münster, Germany
- German Center of Infection Research, Münster University, Corrensstrasse 48, 48149 Münster, Germany
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3
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Mayol GF, Defelipe LA, Arcon JP, Turjanski AG, Marti MA. Solvent Sites Improve Docking Performance of Protein–Protein Complexes and Protein–Protein Interface-Targeted Drugs. J Chem Inf Model 2022; 62:3577-3588. [DOI: 10.1021/acs.jcim.2c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gonzalo F. Mayol
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Lucas A. Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
- European Molecular Biology Laboratory - Hamburg Unit, Notkestrasse 85, Hamburg 22607, Germany
| | - Juan Pablo Arcon
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Spain
- The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
| | - Adrian G. Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Marcelo A. Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
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4
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Norton D, Bonnette WG, Callahan JF, Carr MG, Griffiths-Jones CM, Heightman TD, Kerns JK, Nie H, Rich SJ, Richardson C, Rumsey W, Sanchez Y, Verdonk ML, Willems HMG, Wixted WE, Wolfe L, Woolford AJA, Wu Z, Davies TG. Fragment-Guided Discovery of Pyrazole Carboxylic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2 Related Factor 2 (KEAP1:NRF2) Protein-Protein Interaction. J Med Chem 2021; 64:15949-15972. [PMID: 34705450 DOI: 10.1021/acs.jmedchem.1c01351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The NRF2-mediated cytoprotective response is central to cellular homoeostasis, and there is increasing interest in developing small-molecule activators of this pathway as therapeutics for diseases involving chronic oxidative stress. The protein KEAP1, which regulates NRF2, is a key point for pharmacological intervention, and we recently described the use of fragment-based drug discovery to develop a tool compound that directly disrupts the protein-protein interaction between NRF2 and KEAP1. We now present the identification of a second, chemically distinct series of KEAP1 inhibitors, which provided an alternative chemotype for lead optimization. Pharmacophoric information from our original fragment screen was used to identify new hit matter through database searching and to evolve this into a new lead with high target affinity and cell-based activity. We highlight how knowledge obtained from fragment-based approaches can be used to focus additional screening campaigns in order to de-risk projects through the rapid identification of novel chemical series.
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Affiliation(s)
- David Norton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - William G Bonnette
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - James F Callahan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Maria G Carr
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Tom D Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Jeffrey K Kerns
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Hong Nie
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Sharna J Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - William Rumsey
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Yolanda Sanchez
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Marcel L Verdonk
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - William E Wixted
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Lawrence Wolfe
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | | | - Zining Wu
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Thomas G Davies
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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5
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Wilson DM, Deacon AM, Duncton MAJ, Pellicena P, Georgiadis MM, Yeh AP, Arvai AS, Moiani D, Tainer JA, Das D. Fragment- and structure-based drug discovery for developing therapeutic agents targeting the DNA Damage Response. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:130-142. [PMID: 33115610 PMCID: PMC8666131 DOI: 10.1016/j.pbiomolbio.2020.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/13/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022]
Abstract
Cancer will directly affect the lives of over one-third of the population. The DNA Damage Response (DDR) is an intricate system involving damage recognition, cell cycle regulation, DNA repair, and ultimately cell fate determination, playing a central role in cancer etiology and therapy. Two primary therapeutic approaches involving DDR targeting include: combinatorial treatments employing anticancer genotoxic agents; and synthetic lethality, exploiting a sporadic DDR defect as a mechanism for cancer-specific therapy. Whereas, many DDR proteins have proven "undruggable", Fragment- and Structure-Based Drug Discovery (FBDD, SBDD) have advanced therapeutic agent identification and development. FBDD has led to 4 (with ∼50 more drugs under preclinical and clinical development), while SBDD is estimated to have contributed to the development of >200, FDA-approved medicines. Protein X-ray crystallography-based fragment library screening, especially for elusive or "undruggable" targets, allows for simultaneous generation of hits plus details of protein-ligand interactions and binding sites (orthosteric or allosteric) that inform chemical tractability, downstream biology, and intellectual property. Using a novel high-throughput crystallography-based fragment library screening platform, we screened five diverse proteins, yielding hit rates of ∼2-8% and crystal structures from ∼1.8 to 3.2 Å. We consider current FBDD/SBDD methods and some exemplary results of efforts to design inhibitors against the DDR nucleases meiotic recombination 11 (MRE11, a.k.a., MRE11A), apurinic/apyrimidinic endonuclease 1 (APE1, a.k.a., APEX1), and flap endonuclease 1 (FEN1).
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Affiliation(s)
- David M Wilson
- Hasselt University, Biomedical Research Institute, Diepenbeek, Belgium; Boost Scientific, Heusden-Zolder, Belgium; XPose Therapeutics Inc., San Carlos, CA, USA
| | - Ashley M Deacon
- Accelero Biostructures Inc., San Francisco, CA, USA; XPose Therapeutics Inc., San Carlos, CA, USA
| | | | | | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; XPose Therapeutics Inc., San Carlos, CA, USA
| | - Andrew P Yeh
- Accelero Biostructures Inc., San Francisco, CA, USA
| | - Andrew S Arvai
- Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Davide Moiani
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, USA; Department of Molecular and Cellular Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - John A Tainer
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, USA; Department of Molecular and Cellular Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Debanu Das
- Accelero Biostructures Inc., San Francisco, CA, USA; XPose Therapeutics Inc., San Carlos, CA, USA.
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6
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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] [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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7
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Incaviglia I, Frutiger A, Blickenstorfer Y, Treindl F, Ammirati G, Lüchtefeld I, Dreier B, Plückthun A, Vörös J, Reichmuth AM. An Approach for the Real-Time Quantification of Cytosolic Protein-Protein Interactions in Living Cells. ACS Sens 2021; 6:1572-1582. [PMID: 33759497 DOI: 10.1021/acssensors.0c02480] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In recent years, cell-based assays have been frequently used in molecular interaction analysis. Cell-based assays complement traditional biochemical and biophysical methods, as they allow for molecular interaction analysis, mode of action studies, and even drug screening processes to be performed under physiologically relevant conditions. In most cellular assays, biomolecules are usually labeled to achieve specificity. In order to overcome some of the drawbacks associated with label-based assays, we have recently introduced "cell-based molography" as a biosensor for the analysis of specific molecular interactions involving native membrane receptors in living cells. Here, we expand this assay to cytosolic protein-protein interactions. First, we created a biomimetic membrane receptor by tethering one cytosolic interaction partner to the plasma membrane. The artificial construct is then coherently arranged into a two-dimensional pattern within the cytosol of living cells. Thanks to the molographic sensor, the specific interactions between the coherently arranged protein and its endogenous interaction partners become visible in real time without the use of a fluorescent label. This method turns out to be an important extension of cell-based molography because it expands the range of interactions that can be analyzed by molography to those in the cytosol of living cells.
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Affiliation(s)
- Ilaria Incaviglia
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Yves Blickenstorfer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Fridolin Treindl
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Giulia Ammirati
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Ines Lüchtefeld
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Janos Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Andreas M Reichmuth
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, 8092 Zurich, Switzerland
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8
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Zhang S, Garzan A, Haese N, Bostwick R, Martinez-Gzegozewska Y, Rasmussen L, Streblow DN, Haise MT, Pathak AK, Augelli-Szafran CE, Wu M. Pyrimidone inhibitors targeting Chikungunya Virus nsP3 macrodomain by fragment-based drug design. PLoS One 2021; 16:e0245013. [PMID: 33482665 PMCID: PMC7822648 DOI: 10.1371/journal.pone.0245013] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/18/2020] [Indexed: 12/29/2022] Open
Abstract
The macrodomain of nsP3 (nsP3MD) is highly conserved among the alphaviruses and ADP-ribosylhydrolase activity of Chikungunya Virus (CHIKV) nsP3MD is critical for CHIKV viral replication and virulence. No small molecule drugs targeting CHIKV nsP3 have been identified to date. Here we report small fragments that bind to nsP3MD which were discovered by virtually screening a fragment library and X-ray crystallography. These identified fragments share a similar scaffold, 2-pyrimidone-4-carboxylic acid, and are specifically bound to the ADP-ribose binding site of nsP3MD. Among the fragments, 2-oxo-5,6-benzopyrimidine-4-carboxylic acid showed anti-CHIKV activity with an IC50 of 23 μM. Our fragment-based drug discovery approach provides valuable information to further develop a specific and potent nsP3 inhibitor of CHIKV viral replication based on the 2-pyrimidone-4-carboxylic acid scaffold. In silico studies suggest this pyrimidone scaffold could also bind to the macrodomains of other alphaviruses and coronaviruses and thus, have potential pan-antiviral activity.
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Affiliation(s)
- Sixue Zhang
- Drug Discovery Division, Chemistry Department, Southern Research, Birmingham, Alabama, United States of America
| | - Atefeh Garzan
- Drug Discovery Division, Chemistry Department, Southern Research, Birmingham, Alabama, United States of America
| | - Nicole Haese
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Robert Bostwick
- Drug Discovery Division, High-Throughput Screening Center, Southern Research, Birmingham, Alabama, United States of America
| | - Yohanka Martinez-Gzegozewska
- Drug Discovery Division, High-Throughput Screening Center, Southern Research, Birmingham, Alabama, United States of America
| | - Lynn Rasmussen
- Drug Discovery Division, High-Throughput Screening Center, Southern Research, Birmingham, Alabama, United States of America
| | - Daniel N. Streblow
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Mark T. Haise
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Ashish K. Pathak
- Drug Discovery Division, Chemistry Department, Southern Research, Birmingham, Alabama, United States of America
| | - Corinne E. Augelli-Szafran
- Drug Discovery Division, Chemistry Department, Southern Research, Birmingham, Alabama, United States of America
| | - Mousheng Wu
- Drug Discovery Division, Chemistry Department, Southern Research, Birmingham, Alabama, United States of America
- * E-mail:
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9
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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: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [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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10
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Yang Y, Zheng S, Su S, Zhao C, Xu J, Chen H. SyntaLinker: automatic fragment linking with deep conditional transformer neural networks. Chem Sci 2020; 11:8312-8322. [PMID: 34123096 PMCID: PMC8163338 DOI: 10.1039/d0sc03126g] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/21/2020] [Indexed: 12/18/2022] Open
Abstract
Linking fragments to generate a focused compound library for a specific drug target is one of the challenges in fragment-based drug design (FBDD). Hereby, we propose a new program named SyntaLinker, which is based on a syntactic pattern recognition approach using deep conditional transformer neural networks. This state-of-the-art transformer can link molecular fragments automatically by learning from the knowledge of structures in medicinal chemistry databases (e.g. ChEMBL database). Conventionally, linking molecular fragments was viewed as connecting substructures that were predefined by empirical rules. In SyntaLinker, however, the rules of linking fragments can be learned implicitly from known chemical structures by recognizing syntactic patterns embedded in SMILES notations. With deep conditional transformer neural networks, SyntaLinker can generate molecular structures based on a given pair of fragments and additional restrictions. Case studies have demonstrated the advantages and usefulness of SyntaLinker in FBDD.
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Affiliation(s)
- Yuyao Yang
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
- Center of Chemistry and Chemical Biology, Guangzhou Regenerative Medicine and Health Guangdong Laboratory Guangzhou 510530 China
| | - Shuangjia Zheng
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
| | - Shimin Su
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
- Center of Chemistry and Chemical Biology, Guangzhou Regenerative Medicine and Health Guangdong Laboratory Guangzhou 510530 China
| | - Chao Zhao
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
| | - Hongming Chen
- Center of Chemistry and Chemical Biology, Guangzhou Regenerative Medicine and Health Guangdong Laboratory Guangzhou 510530 China
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11
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Wollenhaupt J, Metz A, Barthel T, Lima GMA, Heine A, Mueller U, Klebe G, Weiss MS. F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening. Structure 2020; 28:694-706.e5. [PMID: 32413289 DOI: 10.1016/j.str.2020.04.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/02/2020] [Accepted: 04/23/2020] [Indexed: 11/15/2022]
Abstract
Crystallographic fragment screening (CFS) provides excellent starting points for projects concerned with drug discovery or biochemical tool compound development. One of the fundamental prerequisites for effective CFS is the availability of a versatile fragment library. Here, we report on the assembly of the 1,103-compound F2X-Universal Library and its 96-compound sub-selection, the F2X-Entry Screen. Both represent the available fragment chemistry and are highly diverse in terms of their 3D-pharmacophore variations. Validation of the F2X-Entry Screen in CFS campaigns using endothiapepsin and the Aar2/RNaseH complex yielded hit rates of 30% and 21%, respectively, and revealed versatile binding sites. Dry presentation of the libraries allows CFS campaigns to be carried out with or without the co-solvent DMSO present. Most of the hits in our validation campaigns could be reproduced also in the absence of DMSO. Consequently, CFS can be carried out more efficiently and for a wider range of conditions and targets.
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Affiliation(s)
- Jan Wollenhaupt
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany; Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Alexander Metz
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany
| | - Tatjana Barthel
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany; Freie Universität Berlin, Institute for Chemistry and Biochemistry, Structural Biochemistry Group, Takustr. 5, 14195 Berlin, Germany
| | - Gustavo M A Lima
- MAX IV Laboratory, Macromolecular Crystallography Group, Lund University, 22100 Lund, Sweden
| | - Andreas Heine
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany
| | - Uwe Mueller
- MAX IV Laboratory, Macromolecular Crystallography Group, Lund University, 22100 Lund, Sweden
| | - Gerhard Klebe
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
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12
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Thorpe JH, Wall ID, Sinnamon RH, Taylor AN, Stavenger RA. Cocktailed fragment screening by X-ray crystallography of the antibacterial target undecaprenyl pyrophosphate synthase from Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2020; 76:40-46. [PMID: 31929185 PMCID: PMC6957112 DOI: 10.1107/s2053230x19017199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/24/2019] [Indexed: 11/10/2022] Open
Abstract
Direct soaking of protein crystals with small-molecule fragments grouped into complementary clusters is a useful technique when assessing the potential of a new crystal system to support structure-guided drug discovery. It provides a robustness check prior to any extensive crystal screening, a double check for assay binding cutoffs and structural data for binding pockets that may or may not be picked out in assay measurements. The structural output from this technique for three novel fragment molecules identified to bind to the antibacterial target Acinetobacter baumannii undecaprenyl pyrophosphate synthase are reported, and the different physicochemical requirements of a successful antibiotic are compared with traditional medicines.
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Affiliation(s)
- James H. Thorpe
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Ian D. Wall
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Robert H. Sinnamon
- GlaxoSmithKline, Upper Providence, 1250 South Collegeville Road, PO Box 5089, Collegeville, PA 19426-0989, USA
| | - Amy N. Taylor
- GlaxoSmithKline, Upper Providence, 1250 South Collegeville Road, PO Box 5089, Collegeville, PA 19426-0989, USA
| | - Robert A. Stavenger
- GlaxoSmithKline, Upper Providence, 1250 South Collegeville Road, PO Box 5089, Collegeville, PA 19426-0989, USA
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13
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Liu M, Quinn RJ. Fragment-based screening with natural products for novel anti-parasitic disease drug discovery. Expert Opin Drug Discov 2019; 14:1283-1295. [PMID: 31512943 PMCID: PMC6816479 DOI: 10.1080/17460441.2019.1653849] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction: Fragment-based drug discovery can identify relatively simple compounds with low binding affinity due to fewer binding interactions with protein targets. FBDD reduces the library size and provides simpler starting points for subsequent chemical optimization of initial hits. A much greater proportion of chemical space can be sampled in fragment-based screening compared to larger molecules with typical molecular weights (MWs) of 250-500 g mol-1 used in high-throughput screening (HTS) libraries. Areas covered: The authors cover the role of natural products in fragment-based drug discovery against parasitic disease targets. They review the approaches to develop fragment-based libraries either using natural products or natural product-like compounds. The authors present approaches to fragment-based drug discovery against parasitic diseases and compare these libraries with the 3D attributes of natural products. Expert opinion: To effectively use the three-dimensional properties and the chemical diversity of natural products in fragment-based drug discovery against parasitic diseases, there needs to be a mind-shift. Library design, in the medicinal chemistry area, has acknowledged that escaping flat-land is very important to increase the chances of clinical success. Attempts to increase sp3 richness in fragment libraries are acknowledged. Sufficient low molecular weight natural products are known to create true natural product fragment libraries.
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Affiliation(s)
- Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University , Brisbane , Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University , Brisbane , Australia
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14
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Kanakaveti V, Anoosha P, Sakthivel R, Rayala S, Gromiha M. Influence of Amino Acid Mutations and Small Molecules on Targeted Inhibition of Proteins Involved in Cancer. Curr Top Med Chem 2019; 19:457-466. [DOI: 10.2174/1568026619666190304143354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/19/2018] [Accepted: 12/28/2018] [Indexed: 12/23/2022]
Abstract
Background:Protein-protein interactions (PPIs) are of crucial importance in regulating the biological processes of cells both in normal and diseased conditions. Significant progress has been made in targeting PPIs using small molecules and achieved promising results. However, PPI drug discovery should be further accelerated with better understanding of chemical space along with various functional aspects.Objective:In this review, we focus on the advancements in computational research for targeted inhibition of protein-protein interactions involved in cancer.Methods:Here, we mainly focused on two aspects: (i) understanding the key roles of amino acid mutations in epidermal growth factor receptor (EGFR) as well as mutation-specific inhibitors and (ii) design of small molecule inhibitors for Bcl-2 to disrupt PPIs.Results:The paradigm of PPI inhibition to date reflect the certainty that inclination towards novel and versatile strategies enormously dictate the success of PPI inhibition. As the chemical space highly differs from the normal drug like compounds the lead optimization process has to be given the utmost priority to ensure the clinical success. Here, we provided a broader perspective on effect of mutations in oncogene EGFR connected to Bcl-2 PPIs and focused on the potential challenges.Conclusion:Understanding and bridging mutations and altered PPIs will provide insights into the alarming signals leading to massive malfunctioning of a biological system in various diseases. Finding rational elucidations from a pharmaceutical stand point will presumably broaden the horizons in future.
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Affiliation(s)
- V. Kanakaveti
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai - 600036, Tamil Nadu, India
| | - P. Anoosha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai - 600036, Tamil Nadu, India
| | - R. Sakthivel
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai - 600036, Tamil Nadu, India
| | - S.K. Rayala
- Molecular Oncology Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai - 600036, Tamil Nadu, India
| | - M.M. Gromiha
- Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
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15
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Wood DJ, Lopez-Fernandez JD, Knight LE, Al-Khawaldeh I, Gai C, Lin S, Martin MP, Miller DC, Cano C, Endicott JA, Hardcastle IR, Noble MEM, Waring MJ. FragLites-Minimal, Halogenated Fragments Displaying Pharmacophore Doublets. An Efficient Approach to Druggability Assessment and Hit Generation. J Med Chem 2019; 62:3741-3752. [PMID: 30860382 DOI: 10.1021/acs.jmedchem.9b00304] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Identifying ligand binding sites on proteins is a critical step in target-based drug discovery. Current approaches to this require resource-intensive screening of large libraries of lead-like or fragment molecules. Here, we describe an efficient and effective experimental approach to mapping interaction sites using a set of halogenated compounds expressing paired hydrogen-bonding motifs, termed FragLites. The FragLites identify productive drug-like interactions, which are identified sensitively and unambiguously by X-ray crystallography, exploiting the anomalous scattering of the halogen substituent. This mapping of protein interaction surfaces provides an assessment of druggability and can identify efficient start points for the de novo design of hit molecules incorporating the interacting motifs. The approach is illustrated by mapping cyclin-dependent kinase 2, which successfully identifies orthosteric and allosteric sites. The hits were rapidly elaborated to develop efficient lead-like molecules. Hence, the approach provides a new method of identifying ligand sites, assessing tractability and discovering new leads.
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Affiliation(s)
- Daniel J Wood
- Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K
| | - J Daniel Lopez-Fernandez
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Leanne E Knight
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Islam Al-Khawaldeh
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Conghao Gai
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Shengying Lin
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Mathew P Martin
- Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K
| | - Duncan C Miller
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Céline Cano
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Jane A Endicott
- Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K
| | - Ian R Hardcastle
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Martin E M Noble
- Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K
| | - Michael J Waring
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
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16
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Heightman TD, Callahan JF, Chiarparin E, Coyle JE, Griffiths-Jones C, Lakdawala AS, McMenamin R, Mortenson PN, Norton D, Peakman TM, Rich SJ, Richardson C, Rumsey WL, Sanchez Y, Saxty G, Willems HMG, Wolfe L, Woolford AJA, Wu Z, Yan H, Kerns JK, Davies TG. Structure–Activity and Structure–Conformation Relationships of Aryl Propionic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1/Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1/NRF2) Protein–Protein Interaction. J Med Chem 2019; 62:4683-4702. [DOI: 10.1021/acs.jmedchem.9b00279] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tom D. Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - James F. Callahan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | | | - Joseph E. Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Ami S. Lakdawala
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Rachel McMenamin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Paul N. Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - David Norton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Torren M. Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Sharna J. Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - William L. Rumsey
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Yolanda Sanchez
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Gordon Saxty
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Lawrence Wolfe
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | | | - Zining Wu
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Hongxing Yan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Jeffrey K. Kerns
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Thomas G. Davies
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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17
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Deaton DN, Do Y, Holt J, Jeune MR, Kramer HF, Larkin AL, Orband-Miller LA, Peckham GE, Poole C, Price DJ, Schaller LT, Shen Y, Shewchuk LM, Stewart EL, Stuart JD, Thomson SA, Ward P, Wilson JW, Xu T, Guss JH, Musetti C, Rendina AR, Affleck K, Anders D, Hancock AP, Hobbs H, Hodgson ST, Hutchinson J, Leveridge MV, Nicholls H, Smith IE, Somers DO, Sneddon HF, Uddin S, Cleasby A, Mortenson PN, Richardson C, Saxty G. The discovery of quinoline-3-carboxamides as hematopoietic prostaglandin D synthase (H-PGDS) inhibitors. Bioorg Med Chem 2019; 27:1456-1478. [DOI: 10.1016/j.bmc.2019.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/30/2019] [Accepted: 02/08/2019] [Indexed: 11/30/2022]
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18
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Chen PC, Hennig J. The role of small-angle scattering in structure-based screening applications. Biophys Rev 2018; 10:1295-1310. [PMID: 30306530 PMCID: PMC6233350 DOI: 10.1007/s12551-018-0464-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/04/2018] [Indexed: 12/16/2022] Open
Abstract
In many biomolecular interactions, changes in the assembly states and structural conformations of participants can act as a complementary reporter of binding to functional and thermodynamic assays. This structural information is captured by a number of structural biology and biophysical techniques that are viable either as primary screens in small-scale applications or as secondary screens to complement higher throughput methods. In particular, small-angle X-ray scattering (SAXS) reports the average distance distribution between all atoms after orientational averaging. Such information is important when for example investigating conformational changes involved in inhibitory and regulatory mechanisms where binding events do not necessarily cause functional changes. Thus, we summarise here the current and prospective capabilities of SAXS-based screening in the context of other methods that yield structural information. Broad guidelines are also provided to assist readers in preparing screening protocols that are tailored to available X-ray sources.
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Affiliation(s)
- Po-Chia Chen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
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19
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Huang X, Guo J, Liu Q, Gu Q, Xu J, Zhou H. Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes. MEDCHEMCOMM 2018; 9:1619-1629. [PMID: 30429968 DOI: 10.1039/c8md00148k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/03/2018] [Indexed: 12/21/2022]
Abstract
Discovery of new drug binding sites on well-established targets is of great interest as it facilitates the design of new mechanistic inhibitors to overcome the acquired drug resistance. Small chemical fragments can easily enter and bind to the cavities on the protein surface. Thus, they can be used to probe new druggable pockets in proteins. DNA gyrase plays indispensable roles in DNA replication, and both its GyrA and GyrB subunits are clinically validated antibacterial targets. New mechanistic GyrB inhibitors are urgently desired since the withdrawal of novobiocin from the market by the FDA due to its reduced efficiency and other reasons. Here, a fragment library was screened against the E. coli GyrB ATPase domain by combining affinity- and bioactivity-based approaches. The following X-ray crystallographic efforts were made to determine the cocrystal structures of GyrB with ten fragment hits, and three different binding modes were disclosed. Fortunately, a hydrophobic pocket which is previously unknown was identified by two fragments. Fragments that bind to this pocket were shown to inhibit the ATPase activity as well as the DNA topological transition activity of DNA gyrase in vitro. A set of fragment analogs were screened to explore the binding capacity of this pocket and identify the better starting fragments for lead development. Phylogenetic analysis revealed that this pocket is conserved in most Gram-negative and also many Gram-positive human pathogenic bacteria, implying a broad-spectrum antibacterial potential and a lower risk of mutation. Thus, the novel druggable pocket and the starting fragments provide a novel basis for designing new GyrB-targeting therapeutics.
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Affiliation(s)
- Xiaojie Huang
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Junsong Guo
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Qi Liu
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Qiong Gu
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Jun Xu
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Huihao Zhou
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
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20
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Abstract
The persistence of West Nile virus (WNV) infections throughout the USA since its inception in 1999 and its continuous spread throughout the globe calls for an urgent need of effective treatments and prevention measures. Although the licensing of several WNV vaccines for veterinary use provides a proof of concept, similar efforts on the development of an effective vaccine for humans remain still unsuccessful. Increased understanding of biology and pathogenesis of WNV together with recent technological advancements have raised hope that an effective WNV vaccine may be available in the near future. In addition, rapid progress in the structural and functional characterization of WNV and other flaviviral proteins have provided a solid base for the design and development of several classes of inhibitors as potential WNV therapeutics. Moreover, the therapeutic monoclonal antibodies demonstrate an excellent efficacy against WNV in animal models and represent a promising class of WNV therapeutics. However, there are some challenges as to the design and development of a safe and efficient WNV vaccine or therapeutic. In this chapter, we discuss the current approaches, progress, and challenges toward the development of WNV vaccines, therapeutic antibodies, and antiviral drugs.
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21
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W Young D. Using Fragment Based Drug Discovery to Target Epigenetic Regulators in Cancer. ACTA ACUST UNITED AC 2017. [DOI: 10.15406/mojbb.2017.04.00062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Kaplan AR, Brady MR, Maciejewski MW, Kammerer RA, Alexandrescu AT. Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix. Biochemistry 2017; 56:1604-1619. [PMID: 28230348 DOI: 10.1021/acs.biochem.6b00634] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To understand the roles ion pairs play in stabilizing coiled coils, we determined nuclear magnetic resonance structures of GCN4p at three pH values. At pH 6.6, all acidic residues are fully charged; at pH 4.4, they are half-charged, and at pH 1.5, they are protonated and uncharged. The α-helix monomer and coiled coil structures of GCN4p are largely conserved, except for a loosening of the coiled coil quaternary structure with a decrease in pH. Differences going from neutral to acidic pH include (i) an unwinding of the coiled coil superhelix caused by the loss of interchain ion pair contacts, (ii) a small increase in the separation of the monomers in the dimer, (iii) a loosening of the knobs-into-holes packing motifs, and (iv) an increased separation between oppositely charged residues that participate in ion pairs at neutral pH. Chemical shifts (HN, N, C', Cα, and Cβ) of GCN4p display a seven-residue periodicity that is consistent with α-helical structure and is invariant with pH. By contrast, periodicity in hydrogen exchange rates at neutral pH is lost at acidic pH as the exchange mechanism moves into the EX1 regime. On the basis of 1H-15N nuclear Overhauser effect relaxation measurements, the α-helix monomers experience only small increases in picosecond to nanosecond backbone dynamics at acidic pH. By contrast, 13C rotating frame T1 relaxation (T1ρ) data evince an increase in picosecond to nanosecond side-chain dynamics at lower pH, particularly for residues that stabilize the coiled coil dimerization interface through ion pairs. The results on the structure and dynamics of GCNp4 over a range of pH values help rationalize why a single structure at neutral pH poorly predicts the pH dependence of the unfolding stability of the coiled coil.
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Affiliation(s)
- Anne R Kaplan
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, Connecticut 06269-3125, United States
| | - Megan R Brady
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, Connecticut 06269-3125, United States
| | - Mark W Maciejewski
- Department of Molecular Biology and Biophysics, UConn Health , Farmington, Connecticut 06030-3305, United States
| | - Richard A Kammerer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut , 5232 Villigen-PSI, Switzerland
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, Connecticut 06269-3125, United States
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23
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Ju H, Zhang J, Huang B, Kang D, Huang B, Liu X, Zhan P. Inhibitors of Influenza Virus Polymerase Acidic (PA) Endonuclease: Contemporary Developments and Perspectives. J Med Chem 2017; 60:3533-3551. [PMID: 28118010 DOI: 10.1021/acs.jmedchem.6b01227] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Influenza virus (IFV) causes periodic global influenza pandemics, resulting in substantial socioeconomic loss and burden on medical facilities. Yearly variation in the effectiveness of vaccines, slow responsiveness to vaccination in cases of pandemic IFV, and emerging resistance to available drugs highlight the need to develop additional small-molecular inhibitors that act on IFV proteins. One promising target is polymerase acidic (PA) endonuclease, which is a bridged dinuclear metalloenzyme that plays a crucial role in initiating IFV replication. During the past decade, intensive efforts have been made to develop small-molecular inhibitors of this endonuclease as candidate agents for treatment of IFV infection. Here, we review the current status of development of PA endonuclease inhibitors and we discuss the applicability of newer medicinal-chemistry strategies for the discovery more potent, selective, and safer inhibitors.
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Affiliation(s)
- Han Ju
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Bing Huang
- Poultry Institute, Shandong Academy of Agricultural Sciences , 1, Jiaoxiao Road, 250023, Jinan, Shandong, P. R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
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24
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Choi S, Choi KY. Screening-based approaches to identify small molecules that inhibit protein–protein interactions. Expert Opin Drug Discov 2017; 12:293-303. [DOI: 10.1080/17460441.2017.1280456] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sehee Choi
- Translational Research Center for Protein Function Control, Yonsei University, Seoul, Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Kang-Yell Choi
- Translational Research Center for Protein Function Control, Yonsei University, Seoul, Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
- CK Biotechnology Inc., 416 Advanced Science and Technology Center, 50 Yonsei-ro, Seoul, Korea
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25
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The Intersection of Structural and Chemical Biology - An Essential Synergy. Cell Chem Biol 2016; 23:173-182. [PMID: 26933743 DOI: 10.1016/j.chembiol.2015.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/04/2015] [Accepted: 12/04/2015] [Indexed: 12/22/2022]
Abstract
The continual improvement in our ability to generate high resolution structural models of biological molecules has stimulated and supported innovative chemical biology projects that target increasingly challenging ligand interaction sites. In this review we outline some of the recent developments in chemical biology and rational ligand design and show selected examples that illustrate the synergy between these research areas.
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26
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Radeva N, Schiebel J, Wang X, Krimmer SG, Fu K, Stieler M, Ehrmann FR, Metz A, Rickmeyer T, Betz M, Winquist J, Park AY, Huschmann FU, Weiss MS, Mueller U, Heine A, Klebe G. Active Site Mapping of an Aspartic Protease by Multiple Fragment Crystal Structures: Versatile Warheads To Address a Catalytic Dyad. J Med Chem 2016; 59:9743-9759. [PMID: 27726357 DOI: 10.1021/acs.jmedchem.6b01195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Crystallography is frequently used as follow-up method to validate hits identified by biophysical screening cascades. The capacity of crystallography to directly screen fragment libraries is often underestimated, due to its supposed low-throughput and need for high-quality crystals. We applied crystallographic fragment screening to map the protein-binding site of the aspartic protease endothiapepsin by individual soaking experiments. Here, we report on 41 fragments binding to the catalytic dyad and adjacent specificity pockets. The analysis identifies already known warheads but also reveals hydrazide, pyrazole, or carboxylic acid fragments as novel functional groups binding to the dyad. A remarkable swapping of the S1 and S1' pocket between structurally related fragments is explained by either steric demand, required displacement of a well-bound water molecule, or changes of trigonal-planar to tetrahedral geometry of an oxygen functional group in a side chain. Some warheads simultaneously occupying both S1 and S1' are promising starting points for fragment-growing strategies.
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Affiliation(s)
- Nedyalka Radeva
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Johannes Schiebel
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Xiaojie Wang
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Stefan G Krimmer
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Kan Fu
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Martin Stieler
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Frederik R Ehrmann
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Thomas Rickmeyer
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Michael Betz
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Johan Winquist
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Ah Young Park
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Franziska U Huschmann
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, 12489 Berlin, Germany.,MAX IV Laboratory, Lund University , Fotongatan 2, 225 94 Lund, Sweden
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
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27
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Schiebel J, Krimmer SG, Röwer K, Knörlein A, Wang X, Park AY, Stieler M, Ehrmann FR, Fu K, Radeva N, Krug M, Huschmann FU, Glöckner S, Weiss MS, Mueller U, Klebe G, Heine A. High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits. Structure 2016; 24:1398-1409. [PMID: 27452405 DOI: 10.1016/j.str.2016.06.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 11/29/2022]
Abstract
Today the identification of lead structures for drug development often starts from small fragment-like molecules raising the chances to find compounds that successfully pass clinical trials. At the heart of the screening for fragments binding to a specific target, crystallography delivers structural information essential for subsequent drug design. While it is common to search for bound ligands in electron densities calculated directly after an initial refinement cycle, we raise the important question whether this strategy is viable for fragments characterized by low affinities. Here, we describe and provide a collection of high-quality diffraction data obtained from 364 protein crystals treated with diverse fragments. Subsequent data analysis showed that ∼25% of all hits would have been missed without further refining the resulting structures. To enable fast and reliable hit identification, we have designed an automated refinement pipeline that will inspire the development of optimized tools facilitating the successful application of fragment-based methods.
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Affiliation(s)
- Johannes Schiebel
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Stefan G Krimmer
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Karine Röwer
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Anna Knörlein
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Xiaojie Wang
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Ah Young Park
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Martin Stieler
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Frederik R Ehrmann
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Kan Fu
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Nedyalka Radeva
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Michael Krug
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Franziska U Huschmann
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany; Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Steffen Glöckner
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Gerhard Klebe
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
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Guvench O. Computational functional group mapping for drug discovery. Drug Discov Today 2016; 21:1928-1931. [PMID: 27393487 DOI: 10.1016/j.drudis.2016.06.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/23/2016] [Accepted: 06/29/2016] [Indexed: 01/05/2023]
Abstract
Computational functional group mapping (cFGM) is emerging as a high-impact complement to existing widely used experimental and computational structure-based drug discovery methods. cFGM provides comprehensive atomic-resolution 3D maps of the affinity of functional groups that can constitute drug-like molecules for a given target, typically a protein. These 3D maps can be intuitively and interactively visualized by medicinal chemists to rapidly design synthetically accessible ligands. Given that the maps can inform selection of functional groups for affinity, specificity, and pharmacokinetic properties, they are of utility for both the optimization of existing drug candidates and creating novel ones. Here, I review recent advances in cFGM with emphasis on the unique information content in the approach that offers the potential of broadly facilitating structure-based ligand design.
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Affiliation(s)
- Olgun Guvench
- SilcsBio, LLC, 8 Market Street, Suite 300, Baltimore, MD 21202, USA.
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29
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Schiebel J, Radeva N, Krimmer SG, Wang X, Stieler M, Ehrmann FR, Fu K, Metz A, Huschmann FU, Weiss MS, Mueller U, Heine A, Klebe G. Six Biophysical Screening Methods Miss a Large Proportion of Crystallographically Discovered Fragment Hits: A Case Study. ACS Chem Biol 2016; 11:1693-701. [PMID: 27028906 DOI: 10.1021/acschembio.5b01034] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fragment-based lead discovery (FBLD) has become a pillar in drug development. Typical applications of this method comprise at least two biophysical screens as prefilter and a follow-up crystallographic experiment on a subset of fragments. Clearly, structural information is pivotal in FBLD, but a key question is whether such a screening cascade strategy will retrieve the majority of fragment-bound structures. We therefore set out to screen 361 fragments for binding to endothiapepsin, a representative of the challenging group of aspartic proteases, employing six screening techniques and crystallography in parallel. Crystallography resulted in the very high number of 71 structures. Yet alarmingly, 44% of these hits were not detected by any biophysical screening approach. Moreover, any screening cascade, building on the results from two or more screening methods, would have failed to predict at least 73% of these hits. We thus conclude that, at least in the present case, the frequently applied biophysical prescreening filters deteriorate the number of possible X-ray hits while only the immediate use of crystallography enables exhaustive retrieval of a maximum of fragment structures, which represent a rich source guiding hit-to-lead-to-drug evolution.
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Affiliation(s)
- Johannes Schiebel
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Nedyalka Radeva
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Stefan G. Krimmer
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Xiaojie Wang
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Martin Stieler
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Frederik R. Ehrmann
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Kan Fu
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Alexander Metz
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Franziska U. Huschmann
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie,
Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Manfred S. Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie,
Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie,
Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Andreas Heine
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
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30
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Davies TG, Wixted WE, Coyle JE, Griffiths-Jones C, Hearn K, McMenamin R, Norton D, Rich SJ, Richardson C, Saxty G, Willems HMG, Woolford AJA, Cottom JE, Kou JP, Yonchuk JG, Feldser HG, Sanchez Y, Foley JP, Bolognese BJ, Logan G, Podolin PL, Yan H, Callahan JF, Heightman TD, Kerns JK. Monoacidic Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1:NRF2) Protein–Protein Interaction with High Cell Potency Identified by Fragment-Based Discovery. J Med Chem 2016; 59:3991-4006. [DOI: 10.1021/acs.jmedchem.6b00228] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Thomas G. Davies
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - William E. Wixted
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Joseph E. Coyle
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | | | - Keisha Hearn
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - Rachel McMenamin
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - David Norton
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - Sharna J. Rich
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | | | - Gordon Saxty
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | | | | | - Joshua E. Cottom
- GlaxoSmithKline
Pharmaceuticals, 1250 South Collegeville
Road, Collegeville, Pennsylvania 19426, United States
| | - Jen-Pyng Kou
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - John G. Yonchuk
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Heidi G. Feldser
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Yolanda Sanchez
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Joseph P. Foley
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Brian J. Bolognese
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Gregory Logan
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Patricia L. Podolin
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Hongxing Yan
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - James F. Callahan
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Tom D. Heightman
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - Jeffrey K. Kerns
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
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31
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Scott DE, Bayly AR, Abell C, Skidmore J. Small molecules, big targets: drug discovery faces the protein–protein interaction challenge. Nat Rev Drug Discov 2016; 15:533-50. [DOI: 10.1038/nrd.2016.29] [Citation(s) in RCA: 625] [Impact Index Per Article: 78.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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32
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Zander U, Hoffmann G, Cornaciu I, Marquette JP, Papp G, Landret C, Seroul G, Sinoir J, Röwer M, Felisaz F, Rodriguez-Puente S, Mariaule V, Murphy P, Mathieu M, Cipriani F, Márquez JA. Automated harvesting and processing of protein crystals through laser photoablation. Acta Crystallogr D Struct Biol 2016; 72:454-66. [PMID: 27050125 PMCID: PMC4822559 DOI: 10.1107/s2059798316000954] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/16/2016] [Indexed: 01/10/2023] Open
Abstract
Currently, macromolecular crystallography projects often require the use of highly automated facilities for crystallization and X-ray data collection. However, crystal harvesting and processing largely depend on manual operations. Here, a series of new methods are presented based on the use of a low X-ray-background film as a crystallization support and a photoablation laser that enable the automation of major operations required for the preparation of crystals for X-ray diffraction experiments. In this approach, the controlled removal of the mother liquor before crystal mounting simplifies the cryocooling process, in many cases eliminating the use of cryoprotectant agents, while crystal-soaking experiments are performed through diffusion, precluding the need for repeated sample-recovery and transfer operations. Moreover, the high-precision laser enables new mounting strategies that are not accessible through other methods. This approach bridges an important gap in automation and can contribute to expanding the capabilities of modern macromolecular crystallography facilities.
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Affiliation(s)
- Ulrich Zander
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Guillaume Hoffmann
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Irina Cornaciu
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jean-Pierre Marquette
- Structure Design Informatics and Structural Biology, Sanofi, 13 Quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Gergely Papp
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Christophe Landret
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Gaël Seroul
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jérémy Sinoir
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Martin Röwer
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Frank Felisaz
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Sonia Rodriguez-Puente
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Vincent Mariaule
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Peter Murphy
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Magali Mathieu
- Structure Design Informatics and Structural Biology, Sanofi, 13 Quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Florent Cipriani
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - José Antonio Márquez
- Grenoble Outstation, European Molecular Biology Laboratory; Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes–EMBL–CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France
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34
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Poklar Ulrih N. Analytical techniques for the study of polyphenol–protein interactions. Crit Rev Food Sci Nutr 2015; 57:2144-2161. [DOI: 10.1080/10408398.2015.1052040] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Nataša Poklar Ulrih
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia, Ljubljana, Slovenia
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35
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Successful generation of structural information for fragment-based drug discovery. Drug Discov Today 2015; 20:1104-11. [DOI: 10.1016/j.drudis.2015.04.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/12/2015] [Accepted: 04/20/2015] [Indexed: 12/25/2022]
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36
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Deller MC, Rupp B. Models of protein-ligand crystal structures: trust, but verify. J Comput Aided Mol Des 2015; 29:817-36. [PMID: 25665575 PMCID: PMC4531100 DOI: 10.1007/s10822-015-9833-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/29/2015] [Indexed: 11/26/2022]
Abstract
X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.
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Affiliation(s)
- Marc C Deller
- The Joint Center for Structural Genomics, San Diego, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Bernhard Rupp
- , k.-k. Hofkristallamt 991 Audrey Place, Vista, CA, 92084, USA.
- Department of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstr. 41, 6020, Innsbruck, Austria.
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Lolli M, Narramore S, Fishwick CW, Pors K. Refining the chemical toolbox to be fit for educational and practical purpose for drug discovery in the 21st Century. Drug Discov Today 2015; 20:1018-26. [DOI: 10.1016/j.drudis.2015.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 04/08/2015] [Accepted: 04/29/2015] [Indexed: 12/16/2022]
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38
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Fischer M, Shoichet BK, Fraser JS. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. Chembiochem 2015; 16:1560-4. [PMID: 26032594 PMCID: PMC4539595 DOI: 10.1002/cbic.201500196] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 11/08/2022]
Abstract
Interrogating fragment libraries by X-ray crystallography is a powerful strategy for discovering allosteric ligands for protein targets. Cryocooling of crystals should theoretically increase the fraction of occupied binding sites and decrease radiation damage. However, it might also perturb protein conformations that can be accessed at room temperature. Using data from crystals measured consecutively at room temperature and at cryogenic temperature, we found that transient binding sites could be abolished at the cryogenic temperatures employed by standard approaches. Changing the temperature at which the crystallographic data was collected could provide a deliberate perturbation to the equilibrium of protein conformations and help to visualize hidden sites with great potential to allosterically modulate protein function.
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Affiliation(s)
- Marcus Fischer
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., Byers Hall, BH-501, Box 2550, San Francisco, CA 94158 (USA)
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., Byers Hall, BH-501, Box 2550, San Francisco, CA 94158 (USA)
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 600 16th St., Genentech Hall, S472E, Box 2240, San Francisco, CA 94158 (USA).
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39
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Scheuermann J, Neri D. Dual-pharmacophore DNA-encoded chemical libraries. Curr Opin Chem Biol 2015; 26:99-103. [DOI: 10.1016/j.cbpa.2015.02.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/12/2015] [Accepted: 02/19/2015] [Indexed: 12/20/2022]
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40
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Magee TV. Progress in discovery of small-molecule modulators of protein-protein interactions via fragment screening. Bioorg Med Chem Lett 2015; 25:2461-8. [PMID: 25971770 DOI: 10.1016/j.bmcl.2015.04.089] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 04/21/2015] [Accepted: 04/27/2015] [Indexed: 11/16/2022]
Abstract
Protein-protein interactions (PPIs) present a formidable challenge to medicinal chemistry. The extended and open nature of many binding sites at protein interfaces has made it difficult to find useful chemical matter by traditional screening methods using standard screening libraries. This Digest focuses on the progress that has been made in discovering small-molecule modulators for a diverse selection of PPI targets using fragment screening and highlights the utility of this strategy in this context.
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Affiliation(s)
- Thomas V Magee
- Worldwide Medicinal Chemistry, Pfizer Inc, 610 Main Street, Cambridge, MA 02139, USA.
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41
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Abstract
Fragment-based drug design has become an important strategy for drug design and development over the last decade. It has been used with particular success in the development of kinase inhibitors, which are one of the most widely explored classes of drug targets today. The application of fragment-based methods to discovering and optimizing kinase inhibitors can be a complicated and daunting task; however, a general process has emerged that has been highly fruitful. Here a practical outline of the fragment process used in kinase inhibitor design and development is laid out with specific examples. A guide to the overall process from initial discovery through fragment screening, including the difficulties in detection, to the computational methods available for use in optimization of the discovered fragments is reported.
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Affiliation(s)
- Jon A Erickson
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, 46285, USA,
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42
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Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:92-100. [PMID: 25117499 DOI: 10.1016/j.pbiomolbio.2014.08.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/23/2014] [Accepted: 08/02/2014] [Indexed: 11/23/2022]
Abstract
X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this "chemical interrogation" of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility.
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43
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Cleasby A, Yon J, Day PJ, Richardson C, Tickle IJ, Williams PA, Callahan JF, Carr R, Concha N, Kerns JK, Qi H, Sweitzer T, Ward P, Davies TG. Structure of the BTB domain of Keap1 and its interaction with the triterpenoid antagonist CDDO. PLoS One 2014; 9:e98896. [PMID: 24896564 PMCID: PMC4045772 DOI: 10.1371/journal.pone.0098896] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 05/08/2014] [Indexed: 11/22/2022] Open
Abstract
The protein Keap1 is central to the regulation of the Nrf2-mediated cytoprotective response, and is increasingly recognized as an important target for therapeutic intervention in a range of diseases involving excessive oxidative stress and inflammation. The BTB domain of Keap1 plays key roles in sensing environmental electrophiles and in mediating interactions with the Cul3/Rbx1 E3 ubiquitin ligase system, and is believed to be the target for several small molecule covalent activators of the Nrf2 pathway. However, despite structural information being available for several BTB domains from related proteins, there have been no reported crystal structures of Keap1 BTB, and this has precluded a detailed understanding of its mechanism of action and interaction with antagonists. We report here the first structure of the BTB domain of Keap1, which is thought to contain the key cysteine residue responsible for interaction with electrophiles, as well as structures of the covalent complex with the antagonist CDDO/bardoxolone, and of the constitutively inactive C151W BTB mutant. In addition to providing the first structural confirmation of antagonist binding to Keap1 BTB, we also present biochemical evidence that adduction of Cys 151 by CDDO is capable of inhibiting the binding of Cul3 to Keap1, and discuss how this class of compound might exert Nrf2 activation through disruption of the BTB-Cul3 interface.
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Affiliation(s)
- Anne Cleasby
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | - Jeff Yon
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | | | | | | | - James F. Callahan
- GlaxoSmithKline, King of Prussia, Pennsylvania, United States of America
| | - Robin Carr
- GlaxoSmithKline, Stevenage, United Kingdom
| | - Nestor Concha
- GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
| | - Jeffrey K. Kerns
- GlaxoSmithKline, King of Prussia, Pennsylvania, United States of America
| | - Hongwei Qi
- GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
| | - Thomas Sweitzer
- GlaxoSmithKline, King of Prussia, Pennsylvania, United States of America
| | - Paris Ward
- GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
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44
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Fechner P, Bleher O, Ewald M, Freudenberger K, Furin D, Hilbig U, Kolarov F, Krieg K, Leidner L, Markovic G, Proll G, Pröll F, Rau S, Riedt J, Schwarz B, Weber P, Widmaier J. Size does matter! Label-free detection of small molecule-protein interaction. Anal Bioanal Chem 2014; 406:4033-51. [PMID: 24817356 DOI: 10.1007/s00216-014-7834-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/07/2014] [Accepted: 04/11/2014] [Indexed: 11/28/2022]
Abstract
This review is focused on methods for detecting small molecules and, in particular, the characterisation of their interaction with natural proteins (e.g. receptors, ion channels). Because there are intrinsic advantages to using label-free methods over labelled methods (e.g. fluorescence, radioactivity), this review only covers label-free techniques. We briefly discuss available techniques and their advantages and disadvantages, especially as related to investigating the interaction between small molecules and proteins. The reviewed techniques include well-known and widely used standard analytical methods (e.g. HPLC-MS, NMR, calorimetry, and X-ray diffraction), newer and more specialised analytical methods (e.g. biosensors), biological systems (e.g. cell lines and animal models), and in-silico approaches.
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Affiliation(s)
- Peter Fechner
- Biametrics GmbH, Auf der Morgenstelle 18, 72076, Tübingen, Germany,
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45
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Saxty G, Norton D, Affleck K, Clapham D, Cleasby A, Coyle J, Day P, Frederickson M, Hancock A, Hobbs H, Hutchinson J, Le J, Leveridge M, McMenamin R, Mortenson P, Page L, Richardson C, Russell L, Sherriff E, Teague S, Uddin S, Hodgson S. Identification of orally bioavailable small-molecule inhibitors of hematopoietic prostaglandin D2 synthase using X-ray fragment based drug discovery. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00280b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD. Automating crystallographic structure solution and refinement of protein-ligand complexes. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:144-54. [PMID: 24419387 PMCID: PMC3919266 DOI: 10.1107/s139900471302748x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 10/07/2013] [Indexed: 11/29/2022]
Abstract
High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation.
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Affiliation(s)
- Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Nigel W. Moriarty
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Herbert E. Klei
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Gábor Bunkóczi
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Jeffrey J. Headd
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Airlie J. McCoy
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Robert D. Oeffner
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Randy J. Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | | | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720-1762, USA
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47
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Abstract
X-ray crystallography is an invaluable technique in structure-based drug discovery, including fragment-based drug discovery, because it is the only technique that can provide a complete three dimensional readout of the interaction between the small molecule and its macromolecular target. X-ray diffraction (XRD) techniques can be employed as the sole method for conducting a screen of a fragment library, or it can be employed as the final technique in a screening campaign to confirm putative "hit" compounds identified by a variety of biochemical and/or biophysical screening techniques. Both approaches require an efficient technique to prepare dozens to hundreds of crystals for data collection, and a reproducible way to deliver ligands to the crystal. Here, a general method for screening cocktails of fragments is described. In cases where X-ray crystallography is employed as a method to verify putative hits, the cocktails of fragments described below would simply be replaced with single fragment solutions.
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Affiliation(s)
- Douglas R Davies
- Emerald Bio, 7869 NE Day Road W, Bainbridge Island, WA, 98110, USA,
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48
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Parnell KM, Foulks JM, Nix RN, Clifford A, Bullough J, Luo B, Senina A, Vollmer D, Liu J, McCarthy V, Xu Y, Saunders M, Liu XH, Pearce S, Wright K, O'Reilly M, McCullar MV, Ho KK, Kanner SB. Pharmacologic activation of PKM2 slows lung tumor xenograft growth. Mol Cancer Ther 2013; 12:1453-60. [PMID: 23720766 DOI: 10.1158/1535-7163.mct-13-0026] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Inactivation of the M2 form of pyruvate kinase (PKM2) in cancer cells is associated with increased tumorigenicity. To test the hypothesis that tumor growth may be inhibited through the PKM2 pathway, we generated a series of small-molecule PKM2 activators. The compounds exhibited low nanomolar activity in both biochemical and cell-based PKM2 activity assays. These compounds did not affect the growth of cancer cell lines under normal conditions in vitro, but strongly inhibited the proliferation of multiple lung cancer cell lines when serine was absent from the cell culture media. In addition, PKM2 activators inhibited the growth of an aggressive lung adenocarcinoma xenograft. These findings show that PKM2 activation by small molecules influences the growth of cancer cells in vitro and in vivo, and suggest that such compounds may augment cancer therapies.
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Scott DE, Ehebauer MT, Pukala T, Marsh M, Blundell TL, Venkitaraman AR, Abell C, Hyvönen M. Using a fragment-based approach to target protein-protein interactions. Chembiochem 2013; 14:332-42. [PMID: 23344974 PMCID: PMC3594973 DOI: 10.1002/cbic.201200521] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Indexed: 02/02/2023]
Abstract
The ability to identify inhibitors of protein-protein interactions represents a major challenge in modern drug discovery and in the development of tools for chemical biology. In recent years, fragment-based approaches have emerged as a new methodology in drug discovery; however, few examples of small molecules that are active against chemotherapeutic targets have been published. Herein, we describe the fragment-based approach of targeting the interaction between the tumour suppressor BRCA2 and the recombination enzyme RAD51; it makes use of a screening pipeline of biophysical techniques that we expect to be more generally applicable to similar targets. Disruption of this interaction in vivo is hypothesised to give rise to cellular hypersensitivity to radiation and genotoxic drugs. We have used protein engineering to create a monomeric form of RAD51 by humanising a thermostable archaeal orthologue, RadA, and used this protein for fragment screening. The initial fragment hits were thoroughly validated biophysically by isothermal titration calorimetry (ITC) and NMR techniques and observed by X-ray crystallography to bind in a shallow surface pocket that is occupied in the native complex by the side chain of a phenylalanine from the conserved FxxA interaction motif found in BRCA2. This represents the first report of fragments or any small molecule binding at this protein-protein interaction site.
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Affiliation(s)
- Duncan E Scott
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Matthias T Ehebauer
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Old Addenbrooke's Site, Cambridge, CB2 1GA (UK) E-mail:
| | - Tara Pukala
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - May Marsh
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Old Addenbrooke's Site, Cambridge, CB2 1GA (UK) E-mail:
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Old Addenbrooke's Site, Cambridge, CB2 1GA (UK) E-mail:
| | - Ashok R Venkitaraman
- Hutchison/MRC Research Centre, University of CambridgeHills Road, Cambridge, CB2 0XZ (UK)
| | - Chris Abell
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Old Addenbrooke's Site, Cambridge, CB2 1GA (UK) E-mail:
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50
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Serine is a natural ligand and allosteric activator of pyruvate kinase M2. Nature 2012; 491:458-462. [PMID: 23064226 DOI: 10.1038/nature11540] [Citation(s) in RCA: 463] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Accepted: 08/23/2012] [Indexed: 12/16/2022]
Abstract
Cancer cells exhibit several unique metabolic phenotypes that are critical for cell growth and proliferation. Specifically, they overexpress the M2 isoform of the tightly regulated enzyme pyruvate kinase (PKM2), which controls glycolytic flux, and are highly dependent on de novo biosynthesis of serine and glycine. Here we describe a new rheostat-like mechanistic relationship between PKM2 activity and serine biosynthesis. We show that serine can bind to and activate human PKM2, and that PKM2 activity in cells is reduced in response to serine deprivation. This reduction in PKM2 activity shifts cells to a fuel-efficient mode in which more pyruvate is diverted to the mitochondria and more glucose-derived carbon is channelled into serine biosynthesis to support cell proliferation.
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