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Grin I, Maksymenko K, Wörtwein T, ElGamacy M. The Damietta Server: a comprehensive protein design toolkit. Nucleic Acids Res 2024; 52:W200-W206. [PMID: 38661218 PMCID: PMC11223796 DOI: 10.1093/nar/gkae297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/22/2024] [Accepted: 04/06/2024] [Indexed: 04/26/2024] Open
Abstract
The growing importance of protein design to various research disciplines motivates the development of integrative computational platforms that enhance the accessibility and interoperability of different design tools. To this end, we describe a web-based toolkit that builds on the Damietta protein design engine, which deploys a tensorized energy calculation framework. The Damietta Server seamlessly integrates different design tools, in addition to other tools such as message-passing neural networks and molecular dynamics routines, allowing the user to perform multiple operations on structural models and forward them across tools. The toolkit can be used for tasks such as core or interface design, symmetric design, mutagenic scanning, or conformational sampling, through an intuitive user interface. With the envisioned integration of more tools, the Damietta Server will provide a central resource for protein design and analysis, benefiting basic and applied biomedical research communities. The toolkit is available with no login requirement through https://damietta.de/.
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Affiliation(s)
- Iwan Grin
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Kateryna Maksymenko
- Max Planck Institute for Biology, Department of Protein Evolution, Tübingen, Germany
| | - Tobias Wörtwein
- Max Planck Institute for Biology, Department of Protein Evolution, Tübingen, Germany
- Division of Translational Oncology, Internal Medicine II, University Hospital Tübingen, Tübingen, Germany
| | - Mohammad ElGamacy
- Max Planck Institute for Biology, Department of Protein Evolution, Tübingen, Germany
- Division of Translational Oncology, Internal Medicine II, University Hospital Tübingen, Tübingen, Germany
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2
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Maksymenko K, Maurer A, Aghaallaei N, Barry C, Borbarán-Bravo N, Ullrich T, Dijkstra TM, Hernandez Alvarez B, Müller P, Lupas AN, Skokowa J, ElGamacy M. The design of functional proteins using tensorized energy calculations. CELL REPORTS METHODS 2023; 3:100560. [PMID: 37671023 PMCID: PMC10475850 DOI: 10.1016/j.crmeth.2023.100560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 05/25/2023] [Accepted: 07/21/2023] [Indexed: 09/07/2023]
Abstract
In protein design, the energy associated with a huge number of sequence-conformer perturbations has to be routinely estimated. Hence, enhancing the throughput and accuracy of these energy calculations can profoundly improve design success rates and enable tackling more complex design problems. In this work, we explore the possibility of tensorizing the energy calculations and apply them in a protein design framework. We use this framework to design enhanced proteins with anti-cancer and radio-tracing functions. Particularly, we designed multispecific binders against ligands of the epidermal growth factor receptor (EGFR), where the tested design could inhibit EGFR activity in vitro and in vivo. We also used this method to design high-affinity Cu2+ binders that were stable in serum and could be readily loaded with copper-64 radionuclide. The resulting molecules show superior functional properties for their respective applications and demonstrate the generalizable potential of the described protein design approach.
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Affiliation(s)
- Kateryna Maksymenko
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Andreas Maurer
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image Guided and Functionally Instructed Tumor Therapies,” Eberhard Karls University, 72076 Tübingen, Germany
| | - Narges Aghaallaei
- Division of Translational Oncology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Caroline Barry
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Krieger School of Arts and Sciences, Johns Hopkins University, Washington, DC 20036, USA
| | - Natalia Borbarán-Bravo
- Division of Translational Oncology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Timo Ullrich
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Tjeerd M.H. Dijkstra
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Department for Women’s Health, University Hospital Tübingen, 72076 Tübingen, Germany
- Translational Bioinformatics, University Hospital Tübingen, 72072 Tübingen, Germany
| | | | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Andrei N. Lupas
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Julia Skokowa
- Division of Translational Oncology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Mohammad ElGamacy
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
- Division of Translational Oncology, University Hospital Tübingen, 72076 Tübingen, Germany
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3
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Skokowa J, Hernandez Alvarez B, Coles M, Ritter M, Nasri M, Haaf J, Aghaallaei N, Xu Y, Mir P, Krahl AC, Rogers KW, Maksymenko K, Bajoghli B, Welte K, Lupas AN, Müller P, ElGamacy M. A topological refactoring design strategy yields highly stable granulopoietic proteins. Nat Commun 2022; 13:2948. [PMID: 35618709 PMCID: PMC9135769 DOI: 10.1038/s41467-022-30157-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 04/19/2022] [Indexed: 11/09/2022] Open
Abstract
Protein therapeutics frequently face major challenges, including complicated production, instability, poor solubility, and aggregation. De novo protein design can readily address these challenges. Here, we demonstrate the utility of a topological refactoring strategy to design novel granulopoietic proteins starting from the granulocyte-colony stimulating factor (G-CSF) structure. We change a protein fold by rearranging the sequence and optimising it towards the new fold. Testing four designs, we obtain two that possess nanomolar activity, the most active of which is highly thermostable and protease-resistant, and matches its designed structure to atomic accuracy. While the designs possess starkly different sequence and structure from the native G-CSF, they show specific activity in differentiating primary human haematopoietic stem cells into mature neutrophils. The designs also show significant and specific activity in vivo. Our topological refactoring approach is largely independent of sequence or structural context, and is therefore applicable to a wide range of protein targets. Skokowa et al. reconstruct the fold of a granulopoietic cytokine, resulting in de novo, hyperstable, highly active proteins with therapeutic potential for treating several neutropenia disorders.
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Affiliation(s)
- Julia Skokowa
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany.
| | | | - Murray Coles
- Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Malte Ritter
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Masoud Nasri
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Jérémy Haaf
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Narges Aghaallaei
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Yun Xu
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Perihan Mir
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Ann-Christin Krahl
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Katherine W Rogers
- Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany.,Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kateryna Maksymenko
- Max Planck Institute for Biology, 72076, Tübingen, Germany.,Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany
| | - Baubak Bajoghli
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Karl Welte
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Andrei N Lupas
- Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany.,Department of Biology, University of Konstanz, 78464, Konstanz, Germany
| | - Mohammad ElGamacy
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany. .,Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany. .,Heliopolis Biotechnology Ltd, Cambridge, CB24 9RX, UK. .,Max Planck Institute for Biology, 72076, Tübingen, Germany.
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Decker JS, Menacho-Melgar R, Lynch MD. Integrated autolysis, DNA hydrolysis and precipitation enables an improved bioprocess for Q-Griffithsin, a broad-spectrum antiviral and clinical-stage anti-COVID-19 candidate. Biochem Eng J 2022; 181:108403. [PMID: 35308834 PMCID: PMC8917701 DOI: 10.1016/j.bej.2022.108403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/01/2022] [Accepted: 03/09/2022] [Indexed: 12/03/2022]
Abstract
Across the biomanufacturing industry, innovations are needed to improve efficiency and flexibility, especially in the face of challenges such as the COVID-19 pandemic. Here we report an improved bioprocess for Q-Griffithsin, a broad-spectrum antiviral currently in clinical trials for COVID-19. Q-Griffithsin is produced at high titer in E. coli and purified to anticipated clinical grade without conventional chromatography or the need for any fixed downstream equipment. The process is thus both low-cost and highly flexible, facilitating low sales prices and agile modifications of production capacity, two key features for pandemic response. The simplicity of this process is enabled by a novel unit operation that integrates cellular autolysis, autohydrolysis of nucleic acids, and contaminant precipitation, giving essentially complete removal of host cell DNA as well as reducing host cell proteins and endotoxin by 3.6 and 2.4 log10 units, respectively. This unit operation can be performed rapidly and in the fermentation vessel, such that Q-GRFT is obtained with 100% yield and > 99.9% purity immediately after fermentation and requires only a flow-through membrane chromatography step for further contaminant removal. Using this operation or variations of it may enable improved bioprocesses for a range of other high-value proteins in E. coli.
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Affiliation(s)
- John S Decker
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
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ElGamacy M. Accelerating therapeutic protein design. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:85-118. [PMID: 35534117 DOI: 10.1016/bs.apcsb.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein structures provide for defined microenvironments that can support complex pharmacological functions, otherwise unachievable by small molecules. The advent of therapeutic proteins has thus greatly broadened the range of manageable disorders. Leveraging the knowledge and recent advances in de novo protein design methods has the prospect of revolutionizing how protein drugs are discovered and developed. This review lays out the main challenges facing therapeutic proteins discovery and development, and how present and future advancements of protein design can accelerate the protein drug pipelines.
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Affiliation(s)
- Mohammad ElGamacy
- University Hospital Tübingen, Division of Translational Oncology, Tübingen, Germany; Max Planck Institute for Biology, Tübingen, Germany.
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6
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Decker JS, Menacho-Melgar R, Lynch MD. Integrated Autolysis, DNA Hydrolysis and Precipitation Enables an Improved Bioprocess for Q-Griffithsin, a Broad-Spectrum Antiviral and Clinical-Stage anti-COVID-19 Candidate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.12.30.474602. [PMID: 35018377 PMCID: PMC8750652 DOI: 10.1101/2021.12.30.474602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
UNLABELLED Across the biomanufacturing industry, innovations are needed to improve efficiency and flexibility, especially in the face of challenges such as the COVID-19 pandemic. Here we report an improved bioprocess for Q-Griffithsin, a broad-spectrum antiviral currently in clinical trials for COVID-19. Q-Griffithsin is produced at high titer in E. coli and purified to anticipated clinical grade without conventional chromatography or the need for any fixed downstream equipment. The process is thus both low-cost and highly flexible, facilitating low sales prices and agile modifications of production capacity, two key features for pandemic response. The simplicity of this process is enabled by a novel unit operation that integrates cellular autolysis, autohydrolysis of nucleic acids, and contaminant precipitation, giving essentially complete removal of host cell DNA as well as reducing host cell proteins and endotoxin by 3.6 and 2.4 log 10 units, respectively. This unit operation can be performed rapidly and in the fermentation vessel, such that Q-GRFT is obtained with 100% yield and >99.9% purity immediately after fermentation and requires only a flow-through membrane chromatography step for further contaminant removal. Using this operation or variations of it may enable improved bioprocesses for a range of other high-value proteins in E. coli . HIGHLIGHTS Integrating autolysis, DNA hydrolysis and precipitation enables process simplificationAutolysis reduces endotoxin release and burden to purificationQ-Griffithsin recovered from fermentation vessel at >99.9% purity and 100% yieldQ-Griffithsin purified to anticipated clinical grade without conventional chromatographyThe resulting bioprocess is 100% disposables-compatible, scalable, and low-cost.
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Masrati G, Landau M, Ben-Tal N, Lupas A, Kosloff M, Kosinski J. Integrative Structural Biology in the Era of Accurate Structure Prediction. J Mol Biol 2021; 433:167127. [PMID: 34224746 DOI: 10.1016/j.jmb.2021.167127] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022]
Abstract
Characterizing the three-dimensional structure of macromolecules is central to understanding their function. Traditionally, structures of proteins and their complexes have been determined using experimental techniques such as X-ray crystallography, NMR, or cryo-electron microscopy-applied individually or in an integrative manner. Meanwhile, however, computational methods for protein structure prediction have been improving their accuracy, gradually, then suddenly, with the breakthrough advance by AlphaFold2, whose models of monomeric proteins are often as accurate as experimental structures. This breakthrough foreshadows a new era of computational methods that can build accurate models for most monomeric proteins. Here, we envision how such accurate modeling methods can combine with experimental structural biology techniques, enhancing integrative structural biology. We highlight the challenges that arise when considering multiple structural conformations, protein complexes, and polymorphic assemblies. These challenges will motivate further developments, both in modeling programs and in methods to solve experimental structures, towards better and quicker investigation of structure-function relationships.
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Affiliation(s)
- Gal Masrati
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; European Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Andrei Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| | - Mickey Kosloff
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, 199 Aba Khoushy Ave., Mt. Carmel, 3498838 Haifa, Israel.
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany; Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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