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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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Bouchet-Marquis C, Pagratis M, Kirmse R, Hoenger A. Metallothionein as a clonable high-density marker for cryo-electron microscopy. J Struct Biol 2012; 177:119-27. [PMID: 22068155 PMCID: PMC3261350 DOI: 10.1016/j.jsb.2011.10.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 10/21/2011] [Accepted: 10/24/2011] [Indexed: 11/24/2022]
Abstract
Cryo-electron microscopy is expanding its scope from macromolecules towards much larger and more complex cellular specimens such as organelles, cells and entire tissues. While isolated macromolecular specimens are typically composed of only very few different components that may be recognized by their shape, size or state of polymerization, cellular specimens combine large numbers of proteinaceous structures as well as nucleic acids and lipid arrays. Consequently, an unambiguous identification of these structures within the context of a whole cell may create a very difficult challenge. On plastic-embedded specimens, or Tokuyasu sections (Tokuyasu, 1980), epitopes that are exposed at the surface can be tagged by antibodies. However, vitrified sections have to be kept at strict cryo-conditions (below -140 °C) and therefore do not allow any post-sectioning treatment of the specimens other than data acquisition in the microscope. Hence, the labels have to be placed into the specimen before freezing. Here we report on the application of a small metal-clustering protein, metallothionein (MTH), as a clonable label capable of clustering metal atoms into a high-density particle with high spatial resolution. We tested MTH as a label for kinesin-decorated microtubules (MTs) as well as the building blocks of desmin intermediate filaments (IFs).
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Affiliation(s)
| | | | | | - Andreas Hoenger
- Dept. of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder CO, 80309-0347, USA
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Mathis JM, Bhatia S, Khandelwal A, Kovesdi I, Lokitz SJ, Odaka Y, Takalkar AM, Terry T, Curiel DT. Genetic incorporation of human metallothionein into the adenovirus protein IX for non-invasive SPECT imaging. PLoS One 2011; 6:e16792. [PMID: 21347423 PMCID: PMC3036658 DOI: 10.1371/journal.pone.0016792] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Accepted: 01/14/2011] [Indexed: 11/18/2022] Open
Abstract
As the limits of existing treatments for cancer are recognized, clearly novel therapies must be considered for successful treatment; cancer therapy using adenovirus vectors is a promising strategy. However tracking the biodistribution of adenovirus vectors in vivo is limited to invasive procedures such as biopsies, which are error prone, non-quantitative, and do not give a full representation of the pharmacokinetics involved. Current non-invasive imaging strategies using reporter gene expression have been applied to analyze adenoviral vectors. The major drawback to approaches that tag viruses with reporter genes is that these systems require initial viral infection and subsequent cellular expression of a reporter gene to allow non-invasive imaging. As an alternative to conventional vector detection techniques, we developed a specific genetic labeling system whereby an adenoviral vector incorporates a fusion between capsid protein IX and human metallothionein. Our study herein clearly demonstrates our ability to rescue viable adenoviral particles that display functional metallothionein (MT) as a component of their capsid surface. We demonstrate the feasibility of 99mTc binding in vitro to the pIX-MT fusion on the capsid of adenovirus virions using a simple transchelation reaction. SPECT imaging of a mouse after administration of a 99mTc-radiolabeled virus showed clear localization of radioactivity to the liver. This result strongly supports imaging using pIX-MT, visualizing the normal biodistribution of Ad primarily to the liver upon injection into mice. The ability we have developed to view real-time biodistribution in their physiological milieu represents a significant tool to study adenovirus biology in vivo.
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Affiliation(s)
- J Michael Mathis
- Gene Therapy Program, Department of Cellular Biology, LSU Health Sciences Center, Shreveport, Louisiana, United States of America.
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Nilsson F, Tarli L, Viti F, Neri D. The use of phage display for the development of tumour targeting agents. Adv Drug Deliv Rev 2000; 43:165-96. [PMID: 10967225 DOI: 10.1016/s0169-409x(00)00068-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
One way to improve the selectivity of therapeutic molecules in clinical oncology would be to target them on the tumour site, thereby sparing normal tissues. The development of targeted therapeutic methodologies relies in most cases on the availability of binding molecules specific for tumour-associated markers. The display of repertoires of polypeptides on the surface of filamentous phage, together with the efficient selection-amplification of the desired binding specificities using affinity capture, represents an efficient route towards the isolation of specific peptides and proteins that could act as vehicles for tumour targeting applications. Most investigations in this area of research have so far been performed with phage derived recombinant antibodies, which have been shown to selectively target tumour-associated markers both in preclinical animal models and in the clinic. However, future developments with other classes of polypeptides (small constrained peptides, small globular proteins) promise to be important for the selective delivery of therapeutic agents to the tumour site.
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Affiliation(s)
- F Nilsson
- Institut für Pharmazeutische Wissenschaften, Eidgenössische Technische Hochschule, CH-8057, Zürich, Switzerland
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6
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Neri D, Petrul H, Winter G, Light Y, Marais R, Britton KE, Creighton AM. Radioactive labeling of recombinant antibody fragments by phosphorylation using human casein kinase II and [gamma-32P]-ATP. Nat Biotechnol 1996; 14:485-90. [PMID: 9630925 DOI: 10.1038/nbt0496-485] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A wide range of antibody fragments can be expressed in bacteria and detected immunochemically via peptide tags. Using specially designed tags, we have developed a strategy for radiolabeling antibody fragments secreted from bacteria. Tagged antibody fragments were secreted either into the bacterial periplasm or the culture medium. The tag was not subject to proteolysis either in the broth or in human plasma. After affinity purification the antibody fragments were phosphorylated with [gamma-32P]ATP and casein kinase II. The labeled fragments were used in a gel band-shift assay to measure antigen binding affinities. In contrast to non site-specific methods such as radioiodination, antibodies labeled with casein kinase II retain full immunoreactivity. Radioactively phosphorylated antibody fragments may have many other applications, including radioimmunoassays and radioimmunotherapy.
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Affiliation(s)
- D Neri
- Cambridge Centre for Protein Engineering-MRC Centre, UK.
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George AJ, Jamar F, Tai MS, Heelan BT, Adams GP, McCartney JE, Houston LL, Weiner LM, Oppermann H, Peters AM. Radiometal labeling of recombinant proteins by a genetically engineered minimal chelation site: technetium-99m coordination by single-chain Fv antibody fusion proteins through a C-terminal cysteinyl peptide. Proc Natl Acad Sci U S A 1995; 92:8358-62. [PMID: 7667295 PMCID: PMC41156 DOI: 10.1073/pnas.92.18.8358] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We describe a method to facilitate radioimaging with technetium-99m (99mTc) by genetic incorporation of a 99mTc chelation site in recombinant single-chain Fv (sFv) antibody proteins. This method relies on fusion of the sFv C terminus with a Gly4Cys peptide that specifically coordinates 99mTc. By using analogues of the 26-10 anti-digoxin sFv as our primary model, we find that addition of the chelate peptide, to form 26-10-1 sFv', does not alter the antigen-binding affinity of sFv. We have demonstrated nearly quantitative chelation of 0.5-50 mCi of 99mTc per mg of 26-10-1 sFv' (1 Ci = 37 GBq). These 99mTc-labeled sFv' complexes are highly stable to challenge with saline buffers, plasma, or diethylenetriaminepentaacetic acid. We find that the 99mTc-labeled 741F8-1 sFv', specific for the c-erbB-2 tumor-associated antigen, is effective in imaging human ovarian carcinoma in a scid mouse tumor xenograft model. This fusion chelate methodology should be applicable to diagnostic imaging with 99mTc and radioimmunotherapy with 186Re or 188Re, and its use could extend beyond the sFv' to other engineered antibodies, recombinant proteins, and synthetic peptides.
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Affiliation(s)
- A J George
- Department of Immunology, Royal Postgraduate Medical School, Hammersmith Hospital, London, United Kingdom
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8
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Neri D, Petrul H, Roncucci G. Engineering recombinant antibodies for immunotherapy. CELL BIOPHYSICS 1995; 27:47-61. [PMID: 7493398 DOI: 10.1007/bf02822526] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Recombinant antibody fragments binding with high affinity to their target can be obtained either from hybridomas or directly from antibody libraries on filamentous phage. These fragments are devoid of any activity other than antigen binding, and have to be processed and functionalized in order to be suitable for clinical applications. This article presents the authors' view on the procedures and the features that are important for effective transformation of recombinant antibodies into useful immunotherapeutic agents. The topics presented include phage display methodologies, engineering of high-affinity binding, purification, and functionalization strategies of recombinant antibodies.
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Affiliation(s)
- D Neri
- Cambridge Centre for Protein Engineering, MRC Centre, United Kingdom
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Spooner RA, Deonarain MP, Savage P, Epenetos AA. A universal antibody-derived targeting agent. CELL BIOPHYSICS 1993; 22:225-42. [PMID: 7889540 DOI: 10.1007/bf03033875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We report bacterial expression of a single-chain antibody (ScFv) reactive against the haptens 4-hydroxy-3 nitrophenylacetic acid (NP) and 4-hydroxy-3-iodo-5-nitrophenylacetic acid (NIP) that is suitable for targeting to mammalian cells in vitro in a novel two-step targeting strategy. Hapten-derivatized primary antibodies of known specificity, bound to target cells, can capture the ScFv. Specificity resides in the interaction of the primary targeting antibody with the target and the interaction of the ScFv for NP/NIP, since the ScFv does not bind cells and nonderivatized antibodies bound at cells cannot capture the ScFv. The ScFv described here can therefore be considered as a universal agent for delivery of drugs, toxins, or radionuclides to any cell type for which a previously characterized antibody exists.
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Affiliation(s)
- R A Spooner
- Royal Postgraduate Medical School, Department of Clinical Oncology, Hammersmith Hospital, London
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Das C, Kulkarni PV, Constantinescu A, Antich P, Blattner FR, Tucker PW. Recombinant antibody-metallothionein: design and evaluation for radioimmunoimaging. Proc Natl Acad Sci U S A 1992; 89:9749-53. [PMID: 1409693 PMCID: PMC50210 DOI: 10.1073/pnas.89.20.9749] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We have produced a chimeric antibody (Ab) in which metallothionein, a well-characterized biological chelator of metals, was genetically fused to the F(ab') domain of the S107 Ab heavy chain. Coexpression with the Ab light chain that conveys specificity for the synthetic antigen phosphocholine was achieved in plasmacytoma cells. Metal- and antigen-binding domains of the Ab-metallothionein hybrid function with normal avidity and specificity. Ab-metallothionein can be efficiently loaded with 99mTc and used to specifically bind phosphocholine-haptenated cells in vitro or to localize plasma-cell ascites tumors in mice. The approach offers potential advantages for producing radiolabeled Ab for targeted radiotherapy and diagnostic imaging.
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Affiliation(s)
- C Das
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas 75235
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