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Calinsky R, Levy Y. Histidine in Proteins: pH-Dependent Interplay between π-π, Cation-π, and CH-π Interactions. J Chem Theory Comput 2024. [PMID: 39037905 DOI: 10.1021/acs.jctc.4c00606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Histidine (His) stands out as the most versatile natural amino acid due to its side chain's facile propensity to protonate at physiological pH, leading to a transition from aromatic to cationic characteristics and thereby enabling diverse biomolecular interactions. In this study, our objective was to quantify the energetics and geometries of pairwise interactions involving His at varying pH levels. Through quantum chemical calculations, we discovered that His exhibits robust participation in both π-π and cation-π interactions, underscoring its ability to adopt a π or cationic nature, akin to other common residues. Of particular note, we found that the affinity of protonated His for aromatic residues (via cation-π interactions) is greater than the affinity of neutral His for either cationic residues (also via cation-π interactions) or aromatic residues (via π-π interactions). Furthermore, His frequently engages in CH-π interactions, and notably, depending on its protonation state, we found that some instances of hydrogen bonding by His exhibit greater stability than is typical for interamino acid hydrogen bonds. The strength of the pH-dependent pairwise energies of His with aromatic residues is supported by the abundance of pairwise interactions with His of low and high predicted pKa values. Overall, our findings illustrate the contribution of His interactions to protein stability and its potential involvement in conformational changes despite its relatively low abundance in proteins.
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Affiliation(s)
- Rivka Calinsky
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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2
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Jiang Y, Chiu TP, Mitra R, Rohs R. Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding. Biophys J 2024; 123:248-259. [PMID: 38130056 PMCID: PMC10808038 DOI: 10.1016/j.bpj.2023.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/22/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
DNA recognition and targeting by transcription factors (TFs) through specific binding are fundamental in biological processes. Furthermore, the histidine protonation state at the TF-DNA binding interface can significantly influence the binding mechanism of TF-DNA complexes. Nevertheless, the role of histidine in TF-DNA complexes remains underexplored. Here, we employed all-atom molecular dynamics simulations using AlphaFold2-modeled complexes based on previously solved co-crystal structures to probe the role of the His-12 residue in the Extradenticle (Exd)-Sex combs reduced (Scr)-DNA complex when binding to Scr and Ultrabithorax (Ubx) target sites. Our results demonstrate that the protonation state of histidine notably affected the DNA minor-groove width profile and binding free energy. Examining flanking sequences of various binding affinities derived from SELEX-seq experiments, we analyzed the relationship between binding affinity and specificity. We uncovered how histidine protonation leads to increased binding affinity but can lower specificity. Our findings provide new mechanistic insights into the role of histidine in modulating TF-DNA binding.
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Affiliation(s)
- Yibei Jiang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Tsu-Pei Chiu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Raktim Mitra
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California; Department of Chemistry, University of Southern California, Los Angeles, California; Department of Physics and Astronomy, University of Southern California, Los Angeles, California; Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, California.
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3
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Proteins and their functionalization for finding therapeutic avenues in cancer: Current status and future prospective. Biochim Biophys Acta Rev Cancer 2023; 1878:188862. [PMID: 36791920 DOI: 10.1016/j.bbcan.2023.188862] [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: 06/24/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 02/15/2023]
Abstract
Despite the remarkable advancement in the health care sector, cancer remains the second most fatal disease globally. The existing conventional cancer treatments primarily include chemotherapy, which has been associated with little to severe side effects, and radiotherapy, which is usually expensive. To overcome these problems, target-specific nanocarriers have been explored for delivering chemo drugs. However, recent reports on using a few proteins having anticancer activity and further use of them as drug carriers have generated tremendous attention for furthering the research towards cancer therapy. Biomolecules, especially proteins, have emerged as suitable alternatives in cancer treatment due to multiple favourable properties including biocompatibility, biodegradability, and structural flexibility for easy surface functionalization. Several in vitro and in vivo studies have reported that various proteins derived from animal, plant, and bacterial species, demonstrated strong cytotoxic and antiproliferative properties against malignant cells in native and their different structural conformations. Moreover, surface tunable properties of these proteins help to bind a range of anticancer drugs and target ligands, thus making them efficient delivery agents in cancer therapy. Here, we discuss various proteins obtained from common exogenous sources and how they transform into effective anticancer agents. We also comprehensively discuss the tumor-killing mechanisms of different dietary proteins such as bovine α-lactalbumin, hen egg-white lysozyme, and their conjugates. We also articulate how protein nanostructures can be used as carriers for delivering cancer drugs and theranostics, and strategies to be adopted for improving their in vivo delivery and targeting. We further discuss the FDA-approved protein-based anticancer formulations along with those in different phases of clinical trials.
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4
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Zhang B, Sun J, Yuan Y, Ji D, Sun Y, Liu Y, Li S, Zhu X, Wu X, Hu J, Xie Q, Wu L, Liu L, Cheng B, Zhang Y, Jiang L, Zhao L, Yu F, Song W, Wang M, Xu Y, Ma S, Fei Y, Zhang L, Zhou D, Zhang X. Proximity-enabled covalent binding of IL-2 to IL-2Rα selectively activates regulatory T cells and suppresses autoimmunity. Signal Transduct Target Ther 2023; 8:28. [PMID: 36690610 PMCID: PMC9871032 DOI: 10.1038/s41392-022-01208-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 08/05/2022] [Accepted: 09/20/2022] [Indexed: 01/24/2023] Open
Abstract
Interleukin-2 (IL-2) is a pleiotropic cytokine that orchestrates bidirectional immune responses via regulatory T cells (Tregs) and effector cells, leading to paradoxical consequences. Here, we report a strategy that exploited genetic code expansion-guided incorporation of the latent bioreactive artificial amino acid fluorosulfate-L-tyrosine (FSY) into IL-2 for proximity-enabled covalent binding to IL-2Rα to selectively promote Treg activation. We found that FSY-bearing IL-2 variants, such as L72-FSY, covalently bound to IL-2Rα via sulfur-fluoride exchange when in proximity, resulting in persistent recycling of IL-2 and selectively promoting the expansion of Tregs but not effector cells. Further assessment of L72-FSY-expanded Tregs demonstrated that L72-FSY maintained Tregs in a central memory phenotype without driving terminal differentiation, as demonstrated by simultaneously attenuated expression of lymphocyte activation gene-3 (LAG-3) and enhanced expression of programmed cell death protein-1 (PD-1). Subcutaneous administration of L72-FSY in murine models of pristane-induced lupus and graft-versus-host disease (GvHD) resulted in enhanced and sustained therapeutic efficacy compared with wild-type IL-2 treatment. The efficacy of L72-FSY was further improved by N-terminal PEGylation, which increased its circulatory retention for preferential and sustained effects. This proximity-enabled covalent binding strategy may accelerate the development of pleiotropic cytokines as a new class of immunomodulatory therapies.
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Affiliation(s)
- Bo Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital; Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
| | - Jiaqi Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yeshuang Yuan
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Dezhong Ji
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yeting Sun
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital; Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, The Ministry of Education Key Laboratory, Beijing, 100730, China
| | - Yudong Liu
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Shengjie Li
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital; Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xingxing Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Xunyao Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital; Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jin Hu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital; Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Qiu Xie
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital; Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ling Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Lulu Liu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital; Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Boyang Cheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yuanjie Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Lingjuan Jiang
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital; Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Lidan Zhao
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, The Ministry of Education Key Laboratory, Beijing, 100730, China
| | - Fei Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Wei Song
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital; Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Min Wang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yue Xu
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Shiliang Ma
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yunyun Fei
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, The Ministry of Education Key Laboratory, Beijing, 100730, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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5
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An anti-CD98 antibody displaying pH-dependent Fc-mediated tumour-specific activity against multiple cancers in CD98-humanized mice. Nat Biomed Eng 2023; 7:8-23. [PMID: 36424464 DOI: 10.1038/s41551-022-00956-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 09/27/2022] [Indexed: 11/27/2022]
Abstract
The cell-surface glycoprotein CD98-a subunit of the LAT1/CD98 amino acid transporter-is an attractive target for cancer immunotherapies, but its widespread expression has hampered the development of CD98-targeting antibody therapeutics. Here we report that an anti-CD98 antibody, identified via the screening of phage-display libraries of CD98 single-chain variable fragments with mutated complementarity-determining regions, preserves the physiological function of CD98 and elicits broad-spectrum crystallizable-fragment (Fc)-mediated anti-tumour activity (requiring Fcγ receptors for immunoglobulins, macrophages, dendritic cells and CD8+ T cells, as well as other components of the innate and adaptive immune systems) in multiple xenograft and syngeneic tumour models established in CD98-humanized mice. We also show that a variant of the anti-CD98 antibody with pH-dependent binding, generated by solving the structure of the antibody-CD98 complex, displayed enhanced tumour-specific activity and pharmacokinetics. pH-dependent antibody variants targeting widely expressed antigens may lead to superior therapeutic outcomes.
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6
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Vasic V, Buldun C, Ritz M, Dickopf S, Georges GJ, Spick C, Peuker A, Meier T, Mayer K, Brinkmann U. Targeted chain-exchange-mediated reconstitution of a split type-I cytokine for conditional immunotherapy. MAbs 2023; 15:2245111. [PMID: 37608616 PMCID: PMC10448976 DOI: 10.1080/19420862.2023.2245111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 07/17/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023] Open
Abstract
Antibody-cytokine fusions targeted against tumor-associated antigens (TAAs) are promising cancer immunotherapy agents, with many such molecules currently undergoing clinical trials. However, due to the limited number of tumor-specific targets, on-target off-tumor effects can lead to systemic toxicity. Additionally, targeted cytokines can be scavenged by cytokine receptors on peripheral cells, decreasing tumor penetration. This study aims at overcoming these issues by engineering a platform for targeted conditionally active type I cytokines. Building on our previously reported PACE (Prodrug-Activating Chain Exchange) platform, we split the type I cytokine interleukin-4 (IL-4) to create two inactive IL-4 prodrugs, and fused these split IL-4 counterparts to the C-termini of antibody-like molecules that undergo proximity-induced chain exchange. In doing so, we developed IL-4 prodrugs that preferentially reconstitute into active IL-4 on target cells. We demonstrate that pre-assembled split IL-4 (without additional inactivation) retains activity and present two different strategies of splitting and inactivating IL-4. Using an IL-4 responsive cell-line, we show that IL-4 prodrugs are targeted to TAAs on target cells and regain activity upon chain exchange, primarily in a cis-activation setting. Furthermore, we demonstrate that split IL-4 complementation is also possible in a trans-activation setting, which opens up the possibility for activation of immune cells in the tumor vicinity. We demonstrate that targeted on-cell prodrug conversion is more efficient than nonspecific activation in-solution. Due to the structural similarity between IL-4 and other type I cytokines relevant in cancer immunotherapy such as IL-2, IL-15, and IL-21, cytokine-PACE may be expanded to develop a variety of targeted conditionally active cytokines for cancer immunotherapy.
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Affiliation(s)
- Vedran Vasic
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Can Buldun
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
- Bellevue Asset Management, Küsnacht, Switzerland
| | - Manfred Ritz
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
- Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Steffen Dickopf
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
- Discovery Biology, Morphosys AG, Planegg, Germany
| | - Guy J. Georges
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Christian Spick
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Alessa Peuker
- Reagent Research and Design, Roche Diagnostics GmbH, Penzberg, Germany
| | - Thomas Meier
- Reagent Research and Design, Roche Diagnostics GmbH, Penzberg, Germany
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
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7
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Differential trafficking of ligands trogocytosed via CD28 versus CTLA4 promotes collective cellular control of co-stimulation. Nat Commun 2022; 13:6459. [PMID: 36309492 PMCID: PMC9617924 DOI: 10.1038/s41467-022-34156-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
Intercellular communication is crucial for collective regulation of cellular behaviors. While clustering T cells have been shown to mutually control the production of key communication signals, it is unclear whether they also jointly regulate their availability and degradation. Here we use newly developed reporter systems, bioinformatic analyses, protein structure modeling and genetic perturbations to assess this. We find that T cells utilize trogocytosis by competing antagonistic receptors to differentially control the abundance of immunoregulatory ligands. Specifically, ligands trogocytosed via CD28 are shuttled to the T cell surface, enabling them to co-stimulate neighboring T cells. In contrast, CTLA4-mediated trogocytosis targets ligands for degradation. Mechanistically, this fate separation is controlled by different acid-sensitivities of receptor-ligand interactions and by the receptor intracellular domains. The ability of CD28 and CTLA4 to confer different fates to trogocytosed ligands reveals an additional layer of collective regulation of cellular behaviors and promotes the robustness of population dynamics.
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8
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SpySwitch enables pH- or heat-responsive capture and release for plug-and-display nanoassembly. Nat Commun 2022; 13:3714. [PMID: 35764623 PMCID: PMC9240080 DOI: 10.1038/s41467-022-31193-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
Proteins can be empowered via SpyTag for anchoring and nanoassembly, through covalent bonding to SpyCatcher partners. Here we generate a switchable version of SpyCatcher, allowing gentle purification of SpyTagged proteins. We introduce numerous histidines adjacent to SpyTag’s binding site, giving moderate pH-dependent release. After phage-based selection, our final SpySwitch allows purification of SpyTag- and SpyTag003-fusions from bacterial or mammalian culture by capture at neutral pH and release at pH 5, with purity far beyond His-tag methods. SpySwitch is also thermosensitive, capturing at 4 °C and releasing at 37 °C. With flexible choice of eluent, SpySwitch-purified proteins can directly assemble onto multimeric scaffolds. 60-mer multimerization enhances immunogenicity and we use SpySwitch to purify receptor-binding domains from SARS-CoV-2 and 11 other sarbecoviruses. For these receptor-binding domains we determine thermal resilience (for mosaic vaccine development) and cross-recognition by antibodies. Antibody EY6A reacts across all tested sarbecoviruses, towards potential application against new coronavirus pandemic threats. The SpyCatcher-SpyTag system allows protein anchoring and nanoassembly. Here, the authors engineer SpySwitch, a dually switchable Catcher which allows gentle purification of SpyTagged proteins prior to downstream applications such as the assembly of virus-like particles.
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9
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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: 0] [Impact Index Per Article: 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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10
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An antibody Fc engineered for conditional antibody-dependent cellular cytotoxicity at the low tumor microenvironment pH. J Biol Chem 2022; 298:101798. [PMID: 35248534 PMCID: PMC9006656 DOI: 10.1016/j.jbc.2022.101798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
Despite the exquisite specificity and high affinity of antibody-based cancer therapies, treatment side effects can occur since the tumor-associated antigens targeted are also present on healthy cells. However, the low pH of the tumor microenvironment provides an opportunity to develop conditionally active antibodies with enhanced tumor specificity. Here, we engineered the human IgG1 Fc domain to enhance pH-selective binding to the receptor FcγRIIIa and subsequent antibody-dependent cellular cytotoxicity (ADCC). We displayed the Fc domain on the surface of mammalian cells and generated a site-directed library by altering Fc residues at the Fc-FcγRIIIa interface to support interactions with positively charged histidine residues. We then used a competitive staining and flow cytometric selection strategy to isolate Fc variants exhibiting reduced FcγRIIIa affinities at neutral pH, but physiological affinities at the tumor-typical pH 6.5. We demonstrate that antibodies composed of Fab arms binding the breast cell epithelial marker Her2 and the lead Fc variant, termed acid-Fc, exhibited an ∼2-fold pH-selectivity for FcγRIIIa binding based on the ratio of equilibrium dissociation constants Kd,7.4/Kd,6.5, due to a faster dissociation rate at pH 7.4. Finally, in vitro ADCC assays with human FcγRIIIa-positive natural killer and Her2-positive target cells demonstrated similar activities for anti-Her2 antibodies bearing the wild-type or acid-Fc at pH 6.5, but nearly 20-fold reduced ADCC for acid-Fc at pH 7.4, based on EC50 ratios. This work shows the promise of mammalian cell display for Fc engineering and the feasibility of pH-selective Fc activation to provide a second dimension of selective tumor cell targeting.
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11
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Holder PG, Lim SA, Huang CS, Sharma P, Dagdas YS, Bulutoglu B, Sockolosky JT. Engineering interferons and interleukins for cancer immunotherapy. Adv Drug Deliv Rev 2022; 182:114112. [PMID: 35085624 DOI: 10.1016/j.addr.2022.114112] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 02/08/2023]
Abstract
Cytokines are a class of potent immunoregulatory proteins that are secreted in response to various stimuli and act locally to regulate many aspects of human physiology and disease. Cytokines play important roles in cancer initiation, progression, and elimination, and thus, there is a long clinical history associated with the use of recombinant cytokines to treat cancer. However, the use of cytokines as therapeutics has been limited by cytokine pleiotropy, complex biology, poor drug-like properties, and severe dose-limiting toxicities. Nevertheless, cytokines are crucial mediators of innate and adaptive antitumor immunity and have the potential to enhance immunotherapeutic approaches to treat cancer. Development of immune checkpoint inhibitors and combination immunotherapies has reinvigorated interest in cytokines as therapeutics, and a variety of engineering approaches are emerging to improve the safety and effectiveness of cytokine immunotherapy. In this review we highlight recent advances in cytokine biology and engineering for cancer immunotherapy.
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12
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Zou W, Huang C, Sun Q, Zhao K, Gao H, Su R, Li Y. A stepwise mutagenesis approach using histidine and acidic amino acid to engineer highly pH-dependent protein switches. 3 Biotech 2022; 12:21. [PMID: 34956814 PMCID: PMC8686790 DOI: 10.1007/s13205-021-03079-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 11/26/2021] [Indexed: 10/26/2022] Open
Abstract
Antibody-based drugs can be highly toxic, because they target normal tissue as well as tumor tissue. The pH value of the extracellular microenvironments around tumor tissues is lower than that of normal tissues. Therefore, antibodies that engage in pH-dependent binding at slightly acidic pH are crucial for improving the safety of antibody-based drugs. Thus, we implemented a stepwise mutagenesis approach to engineering pH-dependent antibodies capable of selective binding in the acidic microenvironment in this study. The first step involved single-residue histidine scanning mutagenesis of the antibody's complementarity-determining regions to prescreen for pH-dependent mutants and identify ionizable sensitive hot-spot residues that could be substituted by acidic amino acids to obtain pH-dependent antibodies. The second step involved single-acidic amino acid residue substitutions of the identified residues and the assessment of pH-dependent binding. We identified six ionizable sensitive hot-spot residues using single-histidine scanning mutagenesis. Nine pH-dependent antibodies were isolated using single-acidic amino acid residue mutagenesis at the six hot-spot residue positions. Relative to wild-type anti-CEA chimera antibody, the binding selectivity of the best performing mutant was improved by approximately 32-fold according to ELISA and by tenfold according to FACS assay. The mutant had a high affinity in the pH range of 5.5-6.0. This study supports the development of pH-dependent protein switches and increases our understanding of the role of ionizable residues in protein interfaces. The stepwise mutagenesis approach is rapid, general, and robust and is expected to produce pH-sensitive protein affinity reagents for various applications.
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Affiliation(s)
- Wenjun Zou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Chuncui Huang
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qing Sun
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Keli Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Huanyu Gao
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Rong Su
- Department of Clinical Laboratory, Foshan Hospital of Traditional Chinese Medicine, Foshan, 528000 Guangdong China
| | - Yan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
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13
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Shibuya R, Miyafusa T, Imamura H, Ooishi A, Honda S. Effect of backbone circularization on colloidal stability: Compaction of unfolded structures improves aggregation resistance of granulocyte colony-stimulating factor. Int J Pharm 2021; 605:120774. [PMID: 34116181 DOI: 10.1016/j.ijpharm.2021.120774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/29/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
Aggregation of protein therapeutics can lead to immunogenicity and loss of function in vivo. Its effective prevention requires an understanding of the conformational and colloidal stability of protein and the improvement of both. Granulocyte colony-stimulating factor (G-CSF), which is one of the most widely used protein therapeutics, was previously shown to be conformationally stabilized by connecting its N- and C-termini with amide bonds (backbone circularization). In this study, we investigated whether circularization affects the colloidal stability of proteins. Colloidal stability was indirectly assessed by analyzing the aggregation behavior of G-CSF variants using analytical ultracentrifugation (AUC) and small-angle X-ray scattering (SAXS). Consequently, we found that the unfolded structure of circularized G-CSF was more compact than non-circularized G-CSF, and that backbone circularization improved its aggregation resistance against chemical denaturation by guanidine hydrochloride (GdnHCl). The improved aggregation resistance suggests that the expansion tolerance of circularized G-CSF in the unfolded state increased its colloidal stability. Thus, backbone circularization is an excellent method for enhancing the colloidal and the conformational stability of protein with minimal sequence changes. It is therefore expected to be effective in extending the storage stability of protein therapeutics, enhancing their biological stability.
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Affiliation(s)
- Risa Shibuya
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Takamitsu Miyafusa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hiroshi Imamura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan; Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Ayako Ooishi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shinya Honda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
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14
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Farhat AM, Weiner AC, Posner C, Kim ZS, Orcutt-Jahns B, Carlson SM, Meyer AS. Modeling cell-specific dynamics and regulation of the common gamma chain cytokines. Cell Rep 2021; 35:109044. [PMID: 33910015 PMCID: PMC8179794 DOI: 10.1016/j.celrep.2021.109044] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/01/2020] [Accepted: 04/06/2021] [Indexed: 12/20/2022] Open
Abstract
The γ-chain receptor dimerizes with complexes of the cytokines interleukin-2 (IL-2), IL-4, IL-7, IL-9, IL-15, and IL-21 and their corresponding "private" receptors. These cytokines have existing uses and future potential as immune therapies because of their ability to regulate the abundance and function of specific immune cell populations. Here, we build a binding reaction model for the ligand-receptor interactions of common γ-chain cytokines, which includes receptor trafficking dynamics, enabling quantitative predictions of cell-type-specific response to natural and engineered cytokines. We then show that tensor factorization is a powerful tool to visualize changes in the input-output behavior of the family across time, cell types, ligands, and concentrations. These results present a more accurate model of ligand response validated across a panel of immune cell types as well as a general approach for generating interpretable guidelines for manipulation of cell-type-specific targeting of engineered ligands.
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Affiliation(s)
- Ali M Farhat
- Department of Bioengineering, Jonsson Comprehensive Cancer Center, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Adam C Weiner
- Department of Bioengineering, Jonsson Comprehensive Cancer Center, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | | | - Zoe S Kim
- Department of Bioengineering, Jonsson Comprehensive Cancer Center, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Brian Orcutt-Jahns
- Department of Bioengineering, Jonsson Comprehensive Cancer Center, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | | | - Aaron S Meyer
- Department of Bioengineering, Jonsson Comprehensive Cancer Center, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90024, USA.
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15
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Peletier LA, Jansson-Löfmark R, Gabrielsson J. Comparisons of basic target-mediated drug disposition (TMDD) and ligand facilitated target removal (LFTR). Eur J Pharm Sci 2021; 162:105835. [PMID: 33848634 DOI: 10.1016/j.ejps.2021.105835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/14/2021] [Accepted: 04/02/2021] [Indexed: 11/17/2022]
Abstract
In the well-known model for basic Target-Mediated Drug Disposition (TMDD), drug binds to the target and the resulting drug-target complex is removed by a first order process, leading to loss of both drug and target. In the present note we study what happens when, instead, drug is returned to the free drug pool so that it can a new target molecule. What results is a mechanism in which the drug, here referred to as the ligand, facilitates the removal of the target,and then returns to the free ligand pool. Accordingly the process will be referred to as Ligand-Facilitated Target Removal (LFTR). It is shown through simulations and mathematical analysis how the two models differ and how their signature profiles typically appear. We also derive a useful parameter of both models, the in vivo potency EC50 (L50) which contains both ligand-target binding properties (kon,koff), target turnover (kdeg) and ligand-target complex kinetics (ke(RL)). Thus, this parameter contains a conglomerate of properties and is therefore potentially more informative about relevant (clinical) exposure than the binding affinity (Kd) alone. The derived potency parameter EC50 may therefore be used as a more robust ranking parameter among small and large drug molecules in drug discovery. Subsequently the LFTR model is applied to experimentally obtained literature data and the relevant parameters are estimated.
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Affiliation(s)
- Lambertus A Peletier
- Mathematical Institute, Leiden University, PB 9512, Leiden 2300 RA, the Netherlands.
| | - Rasmus Jansson-Löfmark
- DMPK, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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16
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Sulea T, Rohani N, Baardsnes J, Corbeil CR, Deprez C, Cepero-Donates Y, Robert A, Schrag JD, Parat M, Duchesne M, Jaramillo ML, Purisima EO, Zwaagstra JC. Structure-based engineering of pH-dependent antibody binding for selective targeting of solid-tumor microenvironment. MAbs 2021; 12:1682866. [PMID: 31777319 PMCID: PMC6927761 DOI: 10.1080/19420862.2019.1682866] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Recent development of monoclonal antibodies as mainstream anticancer agents demands further optimization of their safety for use in humans. Potent targeting and/or effector activities on normal tissues is an obvious toxicity concern. Optimization of specific tumor targeting could be achieved by taking advantage of the extracellular acidity of solid tumors relative to normal tissues. Here, we applied a structure-based computational approach to engineer anti-human epidermal growth factor receptor 2 (Her2) antibodies with selective binding in the acidic tumor microenvironment. We used an affinity maturation platform in which dual-pH histidine-scanning mutagenesis was implemented for pH selectivity optimization. Testing of a small set of designs for binding to the recombinant Her2 ectodomain led to the identification of antigen-binding fragment (Fab) variants with the desired pH-dependent binding behavior. Binding selectivity toward acidic pH was improved by as much as 25-fold relative to the parental bH1-Fab. In vitro experiments on cells expressing intact Her2 confirmed that designed variants formatted as IgG1/k full-size antibodies have high affinity and inhibit the growth of tumor spheroids at a level comparable to that of the benchmark anti-Her2 antibody trastuzumab (Herceptin®) at acidic pH, whereas these effects were significantly reduced at physiological pH. In contrast, both Herceptin and the parental bH1 antibody exhibited strong cell binding and growth inhibition irrespective of pH. This work demonstrates the feasibility of computational optimization of antibodies for selective targeting of the acidic environment such as that found in many solid tumors.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Nazanin Rohani
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Christopher R Corbeil
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Christophe Deprez
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yuneivy Cepero-Donates
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Alma Robert
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Joseph D Schrag
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Marie Parat
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mélanie Duchesne
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Maria L Jaramillo
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Enrico O Purisima
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - John C Zwaagstra
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
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17
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Fu G, Yin G, Niu T, Wu W, Han H, Chen H, Yin P. A novel ratiometric fluorescent probe for the detection of mitochondrial pH dynamics during cell damage. Analyst 2021; 146:620-627. [DOI: 10.1039/d0an01240h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A sensitive fluorescent probe (E)-4-(3-(benzo[d]thiazol-2-yl)-4-hydroxy-5-methylstyryl)-1-methylpyridin-1-ium iodide (HBTMP) for the monitoring of pH in mitochondria was rationally exploited.
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Affiliation(s)
- Gaoqing Fu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products
- Ningbo University
- Ningbo
- China
| | - Guoxing Yin
- Key Laboratory of the Assembly and Application of Organic Functional Molecules of Hunan Province
- Hunan Normal University
- Changsha 410081
- China
| | - Tingting Niu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products
- Ningbo University
- Ningbo
- China
| | - Wei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products
- Ningbo University
- Ningbo
- China
| | - Hui Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products
- Ningbo University
- Ningbo
- China
| | - Haimin Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products
- Ningbo University
- Ningbo
- China
| | - Peng Yin
- Key Laboratory of the Assembly and Application of Organic Functional Molecules of Hunan Province
- Hunan Normal University
- Changsha 410081
- China
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18
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Hernandez Alvarez B, Skokowa J, Coles M, Mir P, Nasri M, Maksymenko K, Weidmann L, Rogers KW, Welte K, Lupas AN, Müller P, ElGamacy M. Design of novel granulopoietic proteins by topological rescaffolding. PLoS Biol 2020; 18:e3000919. [PMID: 33351791 PMCID: PMC7755208 DOI: 10.1371/journal.pbio.3000919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 11/24/2020] [Indexed: 11/18/2022] Open
Abstract
Computational protein design is rapidly becoming more powerful, and improving the accuracy of computational methods would greatly streamline protein engineering by eliminating the need for empirical optimization in the laboratory. In this work, we set out to design novel granulopoietic agents using a rescaffolding strategy with the goal of achieving simpler and more stable proteins. All of the 4 experimentally tested designs were folded, monomeric, and stable, while the 2 determined structures agreed with the design models within less than 2.5 Å. Despite the lack of significant topological or sequence similarity to their natural granulopoietic counterpart, 2 designs bound to the granulocyte colony-stimulating factor (G-CSF) receptor and exhibited potent, but delayed, in vitro proliferative activity in a G-CSF-dependent cell line. Interestingly, the designs also induced proliferation and differentiation of primary human hematopoietic stem cells into mature granulocytes, highlighting the utility of our approach to develop highly active therapeutic leads purely based on computational design. De novo designed cytokines that activate the G-CSF receptor show that the receptor-binding information can be encoded onto stable, miniaturised protein scaffolds that possess potent granulopoietic activity; such novel proteins provide for ideal candidates for protein-based therapeutics.
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Affiliation(s)
| | - Julia Skokowa
- University Hospital Tübingen, Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Germany
- * E-mail: (JS); (ME)
| | - Murray Coles
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Perihan Mir
- University Hospital Tübingen, Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Germany
| | - Masoud Nasri
- University Hospital Tübingen, Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Germany
| | | | - Laura Weidmann
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Karl Welte
- University Hospital Tübingen, Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Germany
| | - Andrei N. Lupas
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Patrick Müller
- University Hospital Tübingen, Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Germany
- Friedrich Miescher Laboratory of the Max Planck Society Tübingen, Germany
| | - Mohammad ElGamacy
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- University Hospital Tübingen, Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Germany
- Friedrich Miescher Laboratory of the Max Planck Society Tübingen, Germany
- Heliopolis Biotechnology Ltd., London, United Kingdom
- * E-mail: (JS); (ME)
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19
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Sarkar A, Roitberg AE. pH-Dependent Conformational Changes Lead to a Highly Shifted p Ka for a Buried Glutamic Acid Mutant of SNase. J Phys Chem B 2020; 124:11072-11080. [PMID: 33259714 DOI: 10.1021/acs.jpcb.0c07136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ionizable residues are rarely present in the hydrophobic interior of proteins, but when they are, they play important roles in biological processes such as energy transduction and enzyme catalysis. Internal ionizable residues have anomalous experimental pKa values with respect to their pKa in bulk water. This work investigates the atomistic cause of the highly shifted pKa of the internal Glu23 in the artificially mutated variant V23E of Staphylococcal Nuclease (SNase) using pH replica exchange molecular dynamics (pH-REMD) simulations. The pKa of Glu23 obtained from our calculations is 6.55, which is elevated with respect to the glutamate pKa of 4.40 in bulk water. The calculated value is close to the experimental pKa of 7.10. Our simulations show that the highly shifted pKa of Glu23 is the product of a pH-dependent conformational change, which has been observed experimentally and also seen in our simulations. We carry out an analysis of this pH-dependent conformational change in response to the protonation state change of Glu23. Using a four-state thermodynamic model, we estimate the two conformation-specific pKa values of Glu23 and describe the coupling between the conformational and ionization equilibria.
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Affiliation(s)
- Ankita Sarkar
- Department of Physics, University of Florida, Gainesville, Florida 32611, United States
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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20
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Mishra A, Patil RS, Singh S, Priyanka, Rathore AS. Mechanistic explanation of structural and functional changes induced by methionine mutation in G-CSF protein. CURRENT RESEARCH IN BIOTECHNOLOGY 2020. [DOI: 10.1016/j.crbiot.2020.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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21
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Singh SK, Mishra A, Goel G, Chirmule N, Rathore AS. Modulation of granulocyte colony stimulating factor conformation and receptor binding by methionine oxidation. Proteins 2020; 89:68-80. [PMID: 32860270 DOI: 10.1002/prot.25995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/04/2020] [Accepted: 08/25/2020] [Indexed: 12/16/2022]
Abstract
Biosimilars offer an avenue for potential cost savings and enhanced patient access to various emerging therapies in a budget neutral way. Biosimilars of the granulocyte colony stimulating factor (GCSF) are an excellent example in this regard with as many as 18 versions of the drug being currently approved across globe for treatment of neutropenia. Here, we identified oxidation of the various methionine residues in GCSF as a key heterogeneity that adversely impact its efficacy. In agreement with earlier studies, it was found that oxidation of Met 122 and Met 127 significantly contributes toward reduction of GCSF efficacy, measured using binding affinity to the GCSF receptor. The combination of molecular dynamics simulation along with structural characterization studies established that oxidation of Met 127 and Met 122 brings about a small local conformational change around the B-C loop in GCSF structure due to slight displacement of Asp113 and Thr117 residues. The simulation studies were validated using fluorescence quenching experiments using acrylamide as quencher and site-directed mutagenesis by replacing Met 122 and Met 127 residues with alanine. The results of this study lead to an enhanced mechanistic understanding of the oxidation in GCSF and should be useful in protein engineering efforts to design stable, safe, and efficacious GCSF product. In addition, the structure-function information can provide targets for protein engineering during early drug development and setting specifications of allowable limits of product variants in biosimilar products.
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Affiliation(s)
- Sumit Kumar Singh
- Department of Chemical Engineering, DBT Center of Excellence for Biopharmaceutical Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Avinash Mishra
- Department of Chemical Engineering, DBT Center of Excellence for Biopharmaceutical Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Gaurav Goel
- Department of Chemical Engineering, DBT Center of Excellence for Biopharmaceutical Technology, Indian Institute of Technology Delhi, New Delhi, India
| | | | - Anurag S Rathore
- Department of Chemical Engineering, DBT Center of Excellence for Biopharmaceutical Technology, Indian Institute of Technology Delhi, New Delhi, India
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22
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Jones HM, Tolsma J, Zhang Z, Jasper P, Luo H, Weber GL, Wright K, Bard J, Bell R, Messing D, Kelleher K, Piche-Nicholas N, Webster R. A Physiologically-Based Pharmacokinetic Model for the Prediction of "Half-Life Extension" and "Catch and Release" Monoclonal Antibody Pharmacokinetics. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2020; 9:534-541. [PMID: 32697437 PMCID: PMC7499188 DOI: 10.1002/psp4.12547] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/21/2020] [Indexed: 12/28/2022]
Abstract
Monoclonal antibodies (mAbs) can be engineered to have “extended half‐life” and “catch and release” properties to improve target coverage. We have developed a mAb physiologically‐based pharmacokinetic model that describes intracellular trafficking, neonatal Fc receptor (FcRn) recycling, and nonspecific clearance of mAbs. We extended this model to capture target binding as a function of target affinity, expression, and turnover. For mAbs engineered to have an extended half‐life, the model was able to accurately predict the terminal half‐life (82% within 2‐fold error of the observed value) in the human FcRn transgenic (Tg32) homozygous mouse and human. The model also accurately captures the trend in pharmacokinetic and target coverage data for a set of mAbs with differing catch and release properties in the Tg32 mouse. The mechanistic nature of this model allows us to explore different engineering techniques early in drug discovery, potentially expanding the number of “druggable” targets.
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Affiliation(s)
- Hannah M Jones
- BioMedicine Design, Pfizer Worldwide R&D, Cambridge, Massachusetts, USA
| | | | | | | | - Haobin Luo
- RES Group Inc., Needham, Massachusetts, USA
| | - Gregory L Weber
- BioMedicine Design, Pfizer Worldwide R&D, Cambridge, Massachusetts, USA
| | - Katherine Wright
- BioMedicine Design, Pfizer Worldwide R&D, Andover, Massachusetts, USA
| | - Joel Bard
- BioMedicine Design, Pfizer Worldwide R&D, Cambridge, Massachusetts, USA
| | - Robert Bell
- Rare Disease Research Unit, Pfizer Worldwide R&D, Cambridge, Massachusetts, USA
| | - Dean Messing
- BioMedicine Design, Pfizer Worldwide R&D, Cambridge, Massachusetts, USA
| | - Kerry Kelleher
- BioMedicine Design, Pfizer Worldwide R&D, Cambridge, Massachusetts, USA
| | | | - Robert Webster
- BioMedicine Design, Pfizer Worldwide R&D, Cambridge, Massachusetts, USA
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23
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Martinez-Fabregas J, Wilmes S, Wang L, Hafer M, Pohler E, Lokau J, Garbers C, Cozzani A, Fyfe PK, Piehler J, Kazemian M, Mitra S, Moraga I. Kinetics of cytokine receptor trafficking determine signaling and functional selectivity. eLife 2019; 8:e49314. [PMID: 31774398 PMCID: PMC6914340 DOI: 10.7554/elife.49314] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/24/2019] [Indexed: 12/27/2022] Open
Abstract
Cytokines activate signaling via assembly of cell surface receptors, but it is unclear whether modulation of cytokine-receptor binding parameters can modify biological outcomes. We have engineered IL-6 variants with different affinities to gp130 to investigate how cytokine receptor binding dwell-times influence functional selectivity. Engineered IL-6 variants showed a range of signaling amplitudes and induced biased signaling, with changes in receptor binding dwell-times affecting more profoundly STAT1 than STAT3 phosphorylation. We show that this differential signaling arises from defective translocation of ligand-gp130 complexes to the endosomal compartment and competitive STAT1/STAT3 binding to phospho-tyrosines in gp130, and results in unique patterns of STAT3 binding to chromatin. This leads to a graded gene expression response and differences in ex vivo differentiation of Th17, Th1 and Treg cells. These results provide a molecular understanding of signaling biased by cytokine receptors, and demonstrate that manipulation of signaling thresholds is a useful strategy to decouple cytokine functional pleiotropy.
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Affiliation(s)
- Jonathan Martinez-Fabregas
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Stephan Wilmes
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Luopin Wang
- Department Computer SciencePurdue UniversityWest LafayetteUnited States
| | | | - Elizabeth Pohler
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Juliane Lokau
- Department of Pathology, Medical FacultyOtto-von-Guericke-University MagdeburgMagdeburgGermany
| | - Christoph Garbers
- Department of Pathology, Medical FacultyOtto-von-Guericke-University MagdeburgMagdeburgGermany
| | - Adeline Cozzani
- INSERM UMR-S-11721, Centre de Recherche Jean-Pierre Aubert (JPARC), Institut pour la Recherche sur le Cancer de Lille (IRCL), Université de LilleLilleFrance
| | - Paul K Fyfe
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Jacob Piehler
- Department of BiologyUniversity of OsnabrückOsnabrückGermany
| | - Majid Kazemian
- Department Computer SciencePurdue UniversityWest LafayetteUnited States
| | - Suman Mitra
- INSERM UMR-S-11721, Centre de Recherche Jean-Pierre Aubert (JPARC), Institut pour la Recherche sur le Cancer de Lille (IRCL), Université de LilleLilleFrance
| | - Ignacio Moraga
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
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24
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Shibuya R, Miyafusa T, Honda S. Stabilization of backbone-circularized protein is attained by synergistic gains in enthalpy of folded structure and entropy of unfolded structure. FEBS J 2019; 287:1554-1575. [PMID: 31605655 DOI: 10.1111/febs.15092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/22/2019] [Accepted: 10/10/2019] [Indexed: 11/30/2022]
Abstract
Backbone circularization is an effective technique for protein stabilization. Here, we investigated the effect of a connector, an engineered segment that connects two protein termini, on the conformational stability of previously designed circularized variants of granulocyte colony-stimulating factor (G-CSF). Heat tolerance and chemical denaturation analyses revealed that aggregation resistance and thermodynamic stability of the circularized variants were superior to those of linear G-CSF. Crystal structure and molecular dynamics (MD) simulation of the most thermodynamically stable variant (C166) revealed a high number of intramolecular hydrogen bonds in both the connector region and Helix D adjacent to the connector region in the folded structure. MD simulations and theoretical calculations involving different force fields indicated a reduction in the main chain entropy of C166 in the unfolded state and increase in the intramolecular hydrogen bond energy of C166 in the folded structure. Although backbone circularization is usually considered to alter chain entropy of the unfolded state, the data indicated that it could also improve the conformational enthalpy of the folded state. Further structural examination of the connector region confirmed that protein design based on a statistical analysis of local structures is an effective approach for predicting an optimum connector length to improve the conformational stability of backbone-circularized proteins. Protein design using backbone circularization with an optimum connector length will be useful for the development of effective and safe protein therapeutics. DATABASE: Structural data are available in Protein Data Bank under the accession number 5ZO6.
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Affiliation(s)
- Risa Shibuya
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takamitsu Miyafusa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Shinya Honda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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25
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Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJL, Dougan M, Garcia KC, Baker D. De novo design of potent and selective mimics of IL-2 and IL-15. Nature 2019; 565:186-191. [PMID: 30626941 PMCID: PMC6521699 DOI: 10.1038/s41586-018-0830-7] [Citation(s) in RCA: 310] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/15/2018] [Indexed: 12/28/2022]
Abstract
We describe a de novo computational approach for designing proteins that recapitulate the binding sites of natural cytokines, but are otherwise unrelated in topology or amino acid sequence. We use this strategy to design mimics of the central immune cytokine interleukin-2 (IL-2) that bind to the IL-2 receptor βγc heterodimer (IL-2Rβγc) but have no binding site for IL-2Rα (also called CD25) or IL-15Rα (also known as CD215). The designs are hyper-stable, bind human and mouse IL-2Rβγc with higher affinity than the natural cytokines, and elicit downstream cell signalling independently of IL-2Rα and IL-15Rα. Crystal structures of the optimized design neoleukin-2/15 (Neo-2/15), both alone and in complex with IL-2Rβγc, are very similar to the designed model. Neo-2/15 has superior therapeutic activity to IL-2 in mouse models of melanoma and colon cancer, with reduced toxicity and undetectable immunogenicity. Our strategy for building hyper-stable de novo mimetics could be applied generally to signalling proteins, enabling the creation of superior therapeutic candidates.
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Affiliation(s)
- Daniel-Adriano Silva
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Shawn Yu
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Umut Y Ulge
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jamie B Spangler
- Departments of Biomedical Engineering and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin M Jude
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carlos Labão-Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Lestat R Ali
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alfredo Quijano-Rubio
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Mikel Ruterbusch
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Isabel Leung
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
| | - Tamara Biary
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephanie J Crowley
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Enrique Marcos
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carl D Walkey
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Brian D Weitzner
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Fátima Pardo-Avila
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Javier Castellanos
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Stanley R Riddell
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Michael Dougan
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - K Christopher Garcia
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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26
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Gorman SD, D'Amico RN, Winston DS, Boehr DD. Engineering Allostery into Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:359-384. [PMID: 31707711 PMCID: PMC7508002 DOI: 10.1007/978-981-13-8719-7_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Our ability to engineer protein structure and function has grown dramatically over recent years. Perhaps the next level in protein design is to develop proteins whose function can be regulated in response to various stimuli, including ligand binding, pH changes, and light. Endeavors toward these goals have tested and expanded on our understanding of protein function and allosteric regulation. In this chapter, we provide examples from different methods for developing new allosterically regulated proteins. These methods range from whole insertion of regulatory domains into new host proteins, to covalent attachment of photoswitches to generate light-responsive proteins, and to targeted changes to specific amino acid residues, especially to residues identified to be important for relaying allosteric information across the protein framework. Many of the examples we discuss have already found practical use in medical and biotechnology applications.
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Affiliation(s)
- Scott D Gorman
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Dennis S Winston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
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27
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Lin J, Sagert J. Targeting Drug Conjugates to the Tumor Microenvironment: Probody Drug Conjugates. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/978-3-319-78154-9_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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28
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Sheridan D, Yu ZX, Zhang Y, Patel R, Sun F, Lasaro MA, Bouchard K, Andrien B, Marozsan A, Wang Y, Tamburini P. Design and preclinical characterization of ALXN1210: A novel anti-C5 antibody with extended duration of action. PLoS One 2018; 13:e0195909. [PMID: 29649283 PMCID: PMC5897016 DOI: 10.1371/journal.pone.0195909] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/02/2018] [Indexed: 11/24/2022] Open
Abstract
Eculizumab, a monoclonal antibody (mAb) directed against complement protein C5, is considered to be the current standard of care for patients with paroxysmal nocturnal hemoglobinuria (PNH) and atypical hemolytic uremic syndrome. This study describes the generation and preclinical attributes of ALXN1210, a new long-acting anti-C5 mAb, obtained through select modifications to eculizumab to both largely abolish target-mediated drug disposition (TMDD) and increase recycling efficiency via the neonatal Fc receptor (FcRn). To attenuate the effect of TMDD on plasma terminal half-life (t1/2), histidine substitutions were engineered into the complementarity-determining regions of eculizumab to enhance the dissociation rate of the mAb:C5 complex in the acidic early endosome relative to the slightly basic pH of blood. Antibody variants with optimal pH-dependent binding to C5 exhibited little to no TMDD in mice in the presence of human C5. To further enhance the efficiency of FcRn-mediated recycling of the antibody, two additional substitutions were introduced to increase affinity for human FcRn. These substitutions yielded an additional doubling of the t½ of surrogate anti-mouse C5 antibodies with reduced TMDD in transgenic mice expressing the human FcRn. In conclusion, ALXN1210 is a promising new therapeutic candidate currently in clinical development for treatment of patients with PNH and atypical hemolytic uremic syndrome.
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Affiliation(s)
- Douglas Sheridan
- Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut, United States of America
- * E-mail:
| | - Zhao-Xue Yu
- Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut, United States of America
| | - Yuchun Zhang
- Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut, United States of America
| | - Rekha Patel
- Product Characterization, Alexion Pharmaceuticals, Inc., New Haven, Connecticut, United States of America
| | - Fang Sun
- Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut, United States of America
| | - Melissa A. Lasaro
- Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut, United States of America
| | - Keith Bouchard
- Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut, United States of America
| | - Bruce Andrien
- Early Assay Development, Alexion Pharmaceuticals, Inc., New Haven, Connecticut, United States of America
| | - Andre Marozsan
- Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut, United States of America
| | - Yi Wang
- Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut, United States of America
| | - Paul Tamburini
- Research, Alexion Pharmaceuticals, Inc., New Haven, Connecticut, United States of America
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29
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Weddell JC, Imoukhuede PI. Integrative meta-modeling identifies endocytic vesicles, late endosome and the nucleus as the cellular compartments primarily directing RTK signaling. Integr Biol (Camb) 2018; 9:464-484. [PMID: 28436498 DOI: 10.1039/c7ib00011a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recently, intracellular receptor signaling has been identified as a key component mediating cell responses for various receptor tyrosine kinases (RTKs). However, the extent each endocytic compartment (endocytic vesicle, early endosome, recycling endosome, late endosome, lysosome and nucleus) contributes to receptor signaling has not been quantified. Furthermore, our understanding of endocytosis and receptor signaling is complicated by cell- or receptor-specific endocytosis mechanisms. Therefore, towards understanding the differential endocytic compartment signaling roles, and identifying how to achieve signal transduction control for RTKs, we delineate how endocytosis regulates RTK signaling. We achieve this via a meta-analysis across eight RTKs, integrating computational modeling with experimentally derived cell (compartment volume, trafficking kinetics and pH) and ligand-receptor (ligand/receptor concentration and interaction kinetics) physiology. Our simulations predict the abundance of signaling from eight RTKs, identifying the following hierarchy in RTK signaling: PDGFRβ > IGFR1 > EGFR > PDGFRα > VEGFR1 > VEGFR2 > Tie2 > FGFR1. We find that endocytic vesicles are the primary cell signaling compartment; over 43% of total receptor signaling occurs within the endocytic vesicle compartment for these eight RTKs. Mechanistically, we found that high RTK signaling within endocytic vesicles may be attributed to their low volume (5.3 × 10-19 L) which facilitates an enriched ligand concentration (3.2 μM per ligand molecule within the endocytic vesicle). Under the analyzed physiological conditions, we identified extracellular ligand concentration as the most sensitive parameter to change; hence the most significant one to modify when regulating absolute compartment signaling. We also found that the late endosome and nucleus compartments are important contributors to receptor signaling, where 26% and 18%, respectively, of average receptor signaling occurs across the eight RTKs. Conversely, we found very low membrane-based receptor signaling, exhibiting <1% of the total receptor signaling for these eight RTKs. Moreover, we found that nuclear translocation, mechanistically, requires late endosomal transport; when we blocked receptor trafficking from late endosomes to the nucleus we found a 57% reduction in nuclear translocation. In summary, our research has elucidated the significance of endocytic vesicles, late endosomes and the nucleus in RTK signal propagation.
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Affiliation(s)
- Jared C Weddell
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1304 W Springfield Ave., 3233 Digital Computer Laboratory, Urbana, IL 61801, USA.
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30
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Shlamkovich T, Aharon L, Barton WA, Papo N. Utilizing combinatorial engineering to develop Tie2 targeting antagonistic angiopoetin-2 ligands as candidates for anti-angiogenesis therapy. Oncotarget 2018; 8:33571-33585. [PMID: 28422724 PMCID: PMC5464891 DOI: 10.18632/oncotarget.16827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/24/2017] [Indexed: 11/25/2022] Open
Abstract
In many human cancers, the receptor tyrosine kinase (RTK) Tie2 plays important roles in mediating proliferation, survival, migration and angiogenesis. Thus, molecules that could potently inhibit activation of the Tie2 receptor would have a significant impact on cancer therapy. Nevertheless, attempts to develop Tie2-targeted inhibitors have met with little success, and there is currently no FDA-approved therapeutic selectively targeting Tie2. We used a combinatorial protein engineering approach to develop a new generation of angiopoietin (Ang)2-derived Tie2 antagonists as potential cancer therapeutics and as tools to study angiogenesis. The construct for designing a yeast surface display (YSD) library of potential antagonists was an Ang2 binding domain (Ang2-BD) that retains Tie2 binding ability but prevents ligand multimerization and receptor dimerization and activation. This mutant library was then screened by quantitative high-throughput flow cytometric sorting to identify Ang2-BD variants with increased expression, stability and affinity to Tie2. The selected variants were recombinantly expressed and showed high affinity to soluble and cellular Tie2 and strongly inhibited both Tie2 phosphorylation and endothelial capillary tube formation and cell invasion compared to the parental Ang2-BD. The significance of the study lies in the insight it provides into the sequence-structure-function relationships and mechanism of action of the antagonistic Ang mutants. The approach of using a natural protein ligand as a molecular scaffold for engineering high-affinity agents can be applied to other ligands to create functional protein antagonists against additional biomedical targets.
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Affiliation(s)
- Tomer Shlamkovich
- Department of Biotechnology Engineering, and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lidan Aharon
- Department of Biotechnology Engineering, and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - William A Barton
- Virginia Commonwealth University, Department of Biochemistry and Molecular Biology, Richmond, Virginia, United States of America
| | - Niv Papo
- Department of Biotechnology Engineering, and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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31
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32
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Robinson MJ, Matejtschuk P, Bristow AF, Dalby PA. Tm-Values and Unfolded Fraction Can Predict Aggregation Rates for Granulocyte Colony Stimulating Factor Variant Formulations but Not under Predominantly Native Conditions. Mol Pharm 2017; 15:256-267. [DOI: 10.1021/acs.molpharmaceut.7b00876] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mathew J. Robinson
- Department
of Biochemical Engineering, University College London, London WC1E 7JE, U.K
| | - Paul Matejtschuk
- National Institute
of Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Hertfordshire EN6 3QG, U.K
| | - Adrian F. Bristow
- National Institute
of Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Hertfordshire EN6 3QG, U.K
| | - Paul A. Dalby
- Department
of Biochemical Engineering, University College London, London WC1E 7JE, U.K
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33
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Miyafusa T, Shibuya R, Nishima W, Ohara R, Yoshida C, Honda S. Backbone Circularization Coupled with Optimization of Connecting Segment in Effectively Improving the Stability of Granulocyte-Colony Stimulating Factor. ACS Chem Biol 2017; 12:2690-2696. [PMID: 28895717 DOI: 10.1021/acschembio.7b00776] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Backbone circularization of protein is a powerful method to improve its structural stability. In this paper, we presumed that a tight connection leads to much higher stability. Therefore, we designed circularized variants of a granulocyte-colony stimulating factor (G-CSF) with a structurally optimized terminal connection. To estimate the appropriate length of the connection, we surveyed the Protein Data Bank to find local structures as a model for the connecting segment. We set the library of local structures composed of "helix-loop-helix," subsequently selected entries similar to the G-CSF terminus, and finally sorted the hit structures according to the loop length. Two, five, or nine loop residues were frequently observed; thus, three circularized variants (C163, C166, and C170) were constructed, prepared, and evaluated. All circularized variants demonstrated a higher thermal stability than linear G-CSF (L175). In particular, C166 that retained five connecting residues demonstrated apparent Tm values of 69.4 °C, which is 8.7 °C higher than that of the circularized variant with no truncation (C177), indicating that the optimization of the connecting segment is effective for enhancing the overall structural stability. C166 also showed higher proteolytic stability against both endoprotease and exopeptidase than L175. We anticipate that the present study will contribute to the improvement in the general design of circularized protein and development of G-CSF biobetters.
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Affiliation(s)
- Takamitsu Miyafusa
- Biomedical Research Institute, The National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Risa Shibuya
- Department
of Computational Biology and Medical Sciences, Graduate School of
Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Wataru Nishima
- Biomedical Research Institute, The National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Rie Ohara
- Department
of Computational Biology and Medical Sciences, Graduate School of
Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Chuya Yoshida
- Biomedical Research Institute, The National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shinya Honda
- Biomedical Research Institute, The National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Department
of Computational Biology and Medical Sciences, Graduate School of
Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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34
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Oyler-Yaniv J, Oyler-Yaniv A, Shakiba M, Min NK, Chen YH, Cheng SY, Krichevsky O, Altan-Bonnet N, Altan-Bonnet G. Catch and Release of Cytokines Mediated by Tumor Phosphatidylserine Converts Transient Exposure into Long-Lived Inflammation. Mol Cell 2017; 66:635-647.e7. [PMID: 28575659 PMCID: PMC6611463 DOI: 10.1016/j.molcel.2017.05.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 03/28/2017] [Accepted: 05/08/2017] [Indexed: 01/05/2023]
Abstract
Immune cells constantly survey the host for pathogens or tumors and secrete cytokines to alert surrounding cells of these threats. In vivo, activated immune cells secrete cytokines for several hours, yet an acute immune reaction occurs over days. Given these divergent timescales, we addressed how cytokine-responsive cells translate brief cytokine exposure into phenotypic changes that persist over long timescales. We studied melanoma cell responses to transient exposure to the cytokine interferon γ (IFNγ) by combining a systems-scale analysis of gene expression dynamics with computational modeling and experiments. We discovered that IFNγ is captured by phosphatidylserine (PS) on the surface of viable cells both in vitro and in vivo then slowly released to drive long-term transcription of cytokine-response genes. This mechanism introduces an additional function for PS in dynamically regulating inflammation across diverse cancer and primary cell types and has potential to usher in new immunotherapies targeting PS and inflammatory pathways.
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MESH Headings
- Animals
- Cell Communication
- Cell Line, Tumor
- Coculture Techniques
- Computational Biology
- Computer Simulation
- Databases, Genetic
- Female
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Humans
- Inflammation/genetics
- Inflammation/immunology
- Inflammation/metabolism
- Inflammation/pathology
- Inflammation Mediators/metabolism
- Interferon-gamma/immunology
- Interferon-gamma/metabolism
- Interleukin-12/immunology
- Interleukin-12/metabolism
- Interleukin-23/immunology
- Interleukin-23/metabolism
- Janus Kinases/metabolism
- Lymphocyte Activation
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Lymphocytes, Tumor-Infiltrating/pathology
- Male
- Melanoma, Experimental/genetics
- Melanoma, Experimental/immunology
- Melanoma, Experimental/metabolism
- Melanoma, Experimental/pathology
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Knockout
- Models, Biological
- PTEN Phosphohydrolase/genetics
- PTEN Phosphohydrolase/metabolism
- Phosphatidylserines/immunology
- Phosphatidylserines/metabolism
- Phosphorylation
- RAW 264.7 Cells
- Receptors, Interferon/genetics
- Receptors, Interferon/metabolism
- STAT1 Transcription Factor/metabolism
- Signal Transduction
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocytes/pathology
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/immunology
- Thyroid Neoplasms/metabolism
- Thyroid Neoplasms/pathology
- Time Factors
- Transcription, Genetic
- Interferon gamma Receptor
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Affiliation(s)
- Jennifer Oyler-Yaniv
- ImmunoDynamics Group, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA; Program in Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alon Oyler-Yaniv
- ImmunoDynamics Group, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Physics Department, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Mojdeh Shakiba
- Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Nina K Min
- ImmunoDynamics Group, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ying-Han Chen
- Laboratory of Host-Pathogen Dynamics, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Sheue-Yann Cheng
- Laboratory of Molecular Biology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Oleg Krichevsky
- Physics Department, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel; Ilse Kats Center for Nanoscience, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nihal Altan-Bonnet
- Laboratory of Host-Pathogen Dynamics, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Grégoire Altan-Bonnet
- ImmunoDynamics Group, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA; Program in Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA.
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Kapur S, Silverman AP, Ye AZ, Papo N, Jindal D, Blumenkranz MS, Cochran JR. Engineered ligand-based VEGFR antagonists with increased receptor binding affinity more effectively inhibit angiogenesis. Bioeng Transl Med 2017; 2:81-91. [PMID: 28516164 PMCID: PMC5412928 DOI: 10.1002/btm2.10051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/04/2016] [Accepted: 12/11/2016] [Indexed: 12/22/2022] Open
Abstract
Pathologic angiogenesis is mediated by the coordinated action of the vascular endothelial growth factor (VEGF)/vascular endothelial growth factor receptor 2 (VEGFR2) signaling axis, along with crosstalk contributed by other receptors, notably αvβ3 integrin. We build on earlier work demonstrating that point mutations can be introduced into the homodimeric VEGF ligand to convert it into an antagonist through disruption of binding to one copy of VEGFR2. This inhibitor has limited potency, however, due to loss of avidity effects from bivalent VEGFR2 binding. Here, we used yeast surface display to engineer a variant with VEGFR2 binding affinity approximately 40‐fold higher than the parental antagonist, and 14‐fold higher than the natural bivalent VEGF ligand. Increased VEGFR2 binding affinity correlated with the ability to more effectively inhibit VEGF‐mediated signaling, both in vitro and in vivo, as measured using VEGFR2 phosphorylation and Matrigel implantation assays. High affinity mutations found in this variant were then incorporated into a dual‐specific antagonist that we previously designed to simultaneously bind to and inhibit VEGFR2 and αvβ3 integrin. The resulting dual‐specific protein bound to human and murine endothelial cells with relative affinities of 120 ± 10 pM and 360 ± 50 pM, respectively, which is at least 30‐fold tighter than wild‐type VEGF (3.8 ± 0.5 nM). Finally, we demonstrated that this engineered high‐affinity dual‐specific protein could inhibit angiogenesis in a murine corneal neovascularization model. Taken together, these data indicate that protein engineering strategies can be combined to generate unique antiangiogenic candidates for further clinical development.
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Affiliation(s)
- Shiven Kapur
- Dept. of Bioengineering Stanford University Stanford CA 94303
| | | | - Anne Z Ye
- Dept. of Bioengineering Stanford University Stanford CA 94303
| | - Niv Papo
- Dept. of Bioengineering Stanford University Stanford CA 94303
| | - Darren Jindal
- Dept. of Bioengineering Stanford University Stanford CA 94303
| | - Mark S Blumenkranz
- Dept. of Ophthalmology Byers Eye Institute, Stanford University Stanford CA 94303
| | - Jennifer R Cochran
- Dept. of Bioengineering Stanford University Stanford CA 94303.,Dept. of Chemical Engineering Stanford University Stanford CA 94303.,Stanford Cancer Institute Stanford University Stanford CA 94303
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36
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Enhancement of innate immunity with granulocyte colony-stimulating factor did not mitigate disease in pigs infected with a highly pathogenic Chinese PRRSV strain. Vet Immunol Immunopathol 2016; 179:70-6. [PMID: 27590428 DOI: 10.1016/j.vetimm.2016.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 11/24/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is responsible for one of the most economically important diseases in swine worldwide. It causes reproductive failure in sows and pneumonia in pigs that predisposes them to secondary bacterial infections. Methods to control PRRSV and/or limit secondary bacterial infections are desired to reduce the impact of this virus on animal health. Neutrophils play a major role in combatting infection; they can act as phagocytes as well as produce and release lytic enzymes that have potent antimicrobial effects leading to the destruction and clearance of bacterial pathogens. Granulocyte-colony stimulating factor (G-CSF) is a cytokine that controls the production, differentiation and function of granulocytes (including neutrophils) from the bone marrow. Recent work from our laboratory has shown that encoding porcine G-CSF in a replication-defective adenovirus (Ad5-G-CSF) and delivering a single dose to pigs induced a neutrophilia lasting more than two weeks. As secondary bacterial infection is a common occurrence following PRRSV infection, particularly following challenge with highly pathogenic (HP)-PRRSV, the aim of the current study was to evaluate the effectiveness of a single prophylactic dose of adenovirus-encoded G-CSF to mitigate secondary bacterial disease associated with HP-PRRSV infection. Administration of Ad5-G-CSF induced a significant neutrophilia as expected. However, between 1 and 2days following HP-PRRSV challenge the number of circulating neutrophils decreased dramatically in the HP-PRRSV infected group, but not the non-infected Ad5-G-CSF group. Ad5-G-CSF administration induced monocytosis as well, which was also reduced by HP-PRRSV challenge. There was no difference in the progression of disease between the Ad5-G-CSF and Ad5-empty groups following HP-PRRSV challenge, with pneumonia and systemic bacterial infection occurring in both treatment groups. Given the impact of HP-PRRSV infection on the neutrophilia induced by the Ad5-G-CSF administration, additional studies are warranted to evaluate the timing of Ad5-G-CSF induced neutrophilia and multiple G-CSF inoculations on protection against secondary bacterial infection following PRRSV infection. Nevertheless, this study may provide insight into the pathogenesis of HP-PRRSV.
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37
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Au L, Green DF. Direct Calculation of Protein Fitness Landscapes through Computational Protein Design. Biophys J 2016; 110:75-84. [PMID: 26745411 DOI: 10.1016/j.bpj.2015.11.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/03/2015] [Accepted: 11/16/2015] [Indexed: 11/24/2022] Open
Abstract
Naturally selected amino-acid sequences or experimentally derived ones are often the basis for understanding how protein three-dimensional conformation and function are determined by primary structure. Such sequences for a protein family comprise only a small fraction of all possible variants, however, representing the fitness landscape with limited scope. Explicitly sampling and characterizing alternative, unexplored protein sequences would directly identify fundamental reasons for sequence robustness (or variability), and we demonstrate that computational methods offer an efficient mechanism toward this end, on a large scale. The dead-end elimination and A(∗) search algorithms were used here to find all low-energy single mutant variants, and corresponding structures of a G-protein heterotrimer, to measure changes in structural stability and binding interactions to define a protein fitness landscape. We established consistency between these algorithms with known biophysical and evolutionary trends for amino-acid substitutions, and could thus recapitulate known protein side-chain interactions and predict novel ones.
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Affiliation(s)
- Loretta Au
- Department of Statistics, The University of Chicago, Chicago, Illinois.
| | - David F Green
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York
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38
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Könning D, Zielonka S, Sellmann C, Schröter C, Grzeschik J, Becker S, Kolmar H. Isolation of a pH-Sensitive IgNAR Variable Domain from a Yeast-Displayed, Histidine-Doped Master Library. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:161-167. [PMID: 26838965 DOI: 10.1007/s10126-016-9690-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 12/08/2015] [Indexed: 06/05/2023]
Abstract
In recent years, engineering of pH-sensitivity into antibodies as well as antibody-derived fragments has become more and more attractive for biomedical and biotechnological applications. Herein, we report the isolation of the first pH-sensitive IgNAR variable domain (vNAR), which was isolated from a yeast-displayed, semi-synthetic master library. This strategy enables the direct identification of pH-dependent binders from a histidine-enriched CDR3 library. Displayed vNAR variants contained two histidine substitutions on average at random positions in their 12-residue CDR3 loop. Upon screening of seven rounds against the proof-of-concept target EpCAM (selection for binding at pH 7.4 and decreased binding at pH 6.0), a single clone was obtained that showed specific and pH-dependent binding as characterized by yeast surface display and biolayer interferometry. Potential applications for such pH-dependent vNAR domains include their employment in tailored affinity chromatography, enabling mild elution protocols. Moreover, utilizing a master library for the isolation of pH-sensitive vNAR variants may be a generic strategy to obtain binding entities with prescribed characteristics for applications in biotechnology, diagnostics, and therapy.
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Affiliation(s)
- Doreen Könning
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287, Darmstadt, Germany
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287, Darmstadt, Germany
| | - Carolin Sellmann
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287, Darmstadt, Germany
| | - Christian Schröter
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287, Darmstadt, Germany
| | - Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287, Darmstadt, Germany
| | - Stefan Becker
- Protein Engineering and Antibody Technologies, Merck-Serono, Merck KGaA, Frankfurter Straße 250, D-64293, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287, Darmstadt, Germany.
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Glassman PM, Balthasar JP. Application of a catenary PBPK model to predict the disposition of "catch and release" anti-PCSK9 antibodies. Int J Pharm 2016; 505:69-78. [PMID: 27041125 DOI: 10.1016/j.ijpharm.2016.03.066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/14/2016] [Accepted: 03/31/2016] [Indexed: 10/22/2022]
Abstract
The development of 'catch and release', or pH-sensitive, monoclonal antibodies (mAb) has become of interest to groups seeking to reduce the influence of target-mediated elimination on pharmacokinetics and pharmacodynamics. In this work, a catenary physiologically-based pharmacokinetic (PBPK) model is described to predict the pharmacokinetic benefit conferred by engineering mAbs for 'catch and release' binding. Our previously published PBPK model was adapted for consideration of the production and elimination of proprotein convertase subtilisin/kexin type 9 (PCSK9) in mice, and the model was then applied to predict the pharmacokinetics of anti-PCSK9 mAb with pH-stable (J10) and pH-sensitive binding (J17). The model was able to generate reasonable predictions of both J10 and J17 plasma pharmacokinetics. For J10, mean (±standard deviation) predicted vs. observed areas under the plasma concentration curve (AUCinf) were: 217 (77.1) vs. 103nMday (1mg/kg), 1.14×10(3) (858) vs. 769nMday (3mg/kg), and 6.60×10(3) (5.58×10(3)) vs. 2.86×10(3)nMday (10mg/kg), and for J17 the values were: 838 (161) vs. 818nMday (1mg/kg), 2.30×10(3) (441) vs. 2.57×10(3)nMday (3mg/kg), and 8.42×10(3) (1.50×10(3)) vs. 9.17×10(3)nMday (10mg/kg). Further simulations with the model predicted that target turnover and the magnitude of change in the complex dissociation rate constant between pH 7.4 and pH 6.0 are key determinants of the improvements in pharmacokinetics associated with 'catch and release' mAbs. The model described here may be useful for prediction of the pharmacokinetics of 'catch and release' mAbs directed against other targets.
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Affiliation(s)
- Patrick M Glassman
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14214, United States
| | - Joseph P Balthasar
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14214, United States.
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Mitchell AC, Briquez PS, Hubbell JA, Cochran JR. Engineering growth factors for regenerative medicine applications. Acta Biomater 2016; 30:1-12. [PMID: 26555377 PMCID: PMC6067679 DOI: 10.1016/j.actbio.2015.11.007] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 10/27/2015] [Accepted: 11/06/2015] [Indexed: 01/10/2023]
Abstract
Growth factors are important morphogenetic proteins that instruct cell behavior and guide tissue repair and renewal. Although their therapeutic potential holds great promise in regenerative medicine applications, translation of growth factors into clinical treatments has been hindered by limitations including poor protein stability, low recombinant expression yield, and suboptimal efficacy. This review highlights current tools, technologies, and approaches to design integrated and effective growth factor-based therapies for regenerative medicine applications. The first section describes rational and combinatorial protein engineering approaches that have been utilized to improve growth factor stability, expression yield, biodistribution, and serum half-life, or alter their cell trafficking behavior or receptor binding affinity. The second section highlights elegant biomaterial-based systems, inspired by the natural extracellular matrix milieu, that have been developed for effective spatial and temporal delivery of growth factors to cell surface receptors. Although appearing distinct, these two approaches are highly complementary and involve principles of molecular design and engineering to be considered in parallel when developing optimal materials for clinical applications. STATEMENT OF SIGNIFICANCE Growth factors are promising therapeutic proteins that have the ability to modulate morphogenetic behaviors, including cell survival, proliferation, migration and differentiation. However, the translation of growth factors into clinical therapies has been hindered by properties such as poor protein stability, low recombinant expression yield, and non-physiological delivery, which lead to suboptimal efficacy and adverse side effects. To address these needs, researchers are employing clever molecular and material engineering and design strategies to both improve the intrinsic properties of growth factors and effectively control their delivery into tissue. This review highlights examples of interdisciplinary tools and technologies used to augment the therapeutic potential of growth factors for clinical applications in regenerative medicine.
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Affiliation(s)
- Aaron C Mitchell
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Priscilla S Briquez
- Institute for Bioengineering, School of Life Sciences and School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jeffrey A Hubbell
- Institute for Bioengineering, School of Life Sciences and School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Institute for Molecular Engineering, University of Chicago, Chicago, IL, USA; Materials Science Division, Argonne National Laboratory, Argonne, IL, USA.
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
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Tillotson BJ, Goulatis LI, Parenti I, Duxbury E, Shusta EV. Engineering an Anti-Transferrin Receptor ScFv for pH-Sensitive Binding Leads to Increased Intracellular Accumulation. PLoS One 2015; 10:e0145820. [PMID: 26713870 PMCID: PMC4694649 DOI: 10.1371/journal.pone.0145820] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
The equilibrium binding affinity of receptor-ligand or antibody-antigen pairs may be modulated by protonation of histidine side-chains, and such pH-dependent mechanisms play important roles in biological systems, affecting molecular uptake and trafficking. Here, we aimed to manipulate cellular transport of single-chain antibodies (scFvs) against the transferrin receptor (TfR) by engineering pH-dependent antigen binding. An anti-TfR scFv was subjected to histidine saturation mutagenesis of a single CDR. By employing yeast surface display with a pH-dependent screening pressure, scFvs having markedly increased dissociation from TfR at pH 5.5 were identified. The pH-sensitivity generally resulted from a central cluster of histidine residues in CDRH1. When soluble, pH-sensitive, scFv clone M16 was dosed onto live cells, the internalized fraction was 2.6-fold greater than scFvs that lacked pH-sensitive binding and the increase was dependent on endosomal acidification. Differences in the intracellular distribution of M16 were also observed consistent with an intracellular decoupling of the scFv M16-TfR complex. Engineered pH-sensitive TfR binding could prove important for increasing the effectiveness of TfR-targeted antibodies seeking to exploit endocytosis or transcytosis for drug delivery purposes.
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Affiliation(s)
- Benjamin J. Tillotson
- University of Wisconsin-Madison, Dept. of Chemical and Biological Engineering, Madison, WI, United States of America
| | - Loukas I. Goulatis
- University of Wisconsin-Madison, Dept. of Chemical and Biological Engineering, Madison, WI, United States of America
| | - Isabelle Parenti
- University of Wisconsin-Madison, Dept. of Chemical and Biological Engineering, Madison, WI, United States of America
| | - Elizabeth Duxbury
- University of Wisconsin-Madison, Dept. of Chemical and Biological Engineering, Madison, WI, United States of America
| | - Eric V. Shusta
- University of Wisconsin-Madison, Dept. of Chemical and Biological Engineering, Madison, WI, United States of America
- * E-mail:
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42
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Bioanalytical approaches to assess the proteolytic stability of therapeutic fusion proteins. Bioanalysis 2015; 7:3035-51. [DOI: 10.4155/bio.15.217] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Therapeutic fusion proteins (TFPs) are designed to improve the therapeutic profile of an endogenous protein or protein fragment with a limited dose frequency providing the desired pharmacological activity in vivo. Fusion of a therapeutic protein to a half-life extension or targeting domain can improve the disposition of the molecule or introduce a novel mechanism of action. Prolonged exposure and altered biodistribution of an endogenous protein through fusion technology increases the potential for local protein unfolding during circulation increasing the chance for partial proteolysis of the therapeutic domain. Characterizing the proteolytic liabilities of a TFP can guide engineering efforts to inhibit or hinder partial proteolysis. This review focuses on considerations and techniques for evaluating the stability of a TFP both in vivo and in vitro.
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Bonvin P, Venet S, Fontaine G, Ravn U, Gueneau F, Kosco-Vilbois M, Proudfoot AE, Fischer N. De novo isolation of antibodies with pH-dependent binding properties. MAbs 2015; 7:294-302. [PMID: 25608219 PMCID: PMC4623423 DOI: 10.1080/19420862.2015.1006993] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
pH-dependent antibodies are engineered to release their target at a slightly acidic pH, a property making them suitable for clinical as well as biotechnological applications. Such antibodies were previously obtained by histidine scanning of pre-existing antibodies, a labor-intensive strategy resulting in antibodies that displayed residual binding to their target at pH 6.0. We report here the de novo isolation of pH-dependent antibodies selected by phage display from libraries enriched in histidines. Strongly pH-dependent clones with various affinity profiles against CXCL10 were isolated by this method. Our best candidate has nanomolar affinity for CXCL10 at pH 7.2, but no residual binding was detected at pH 6.0. We therefore propose that this new process is an efficient strategy to generate pH-dependent antibodies.
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Key Words
- BLI, bio-layer interferometry
- CDR, complementary determining region
- CDRH, CDR of the heavy chain
- CDRL, CDR of the light chain
- ELISA, enzyme-linked immunosorbent assay
- GPCR, G protein-coupled receptor
- KB, kinetic buffer
- PBS, phosphate buffered saline
- SPR, surface plasmon resonance
- antibody recycling
- chemokine
- histidine
- mAb, monoclonal antibody
- monoclonal antibody
- pH-dependency
- phage display
- phage libraries
- scFv, single-chain variable fragment
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Heinzelman P, Schoborg JA, Jewett MC. pH responsive granulocyte colony-stimulating factor variants with implications for treating Alzheimer's disease and other central nervous system disorders. Protein Eng Des Sel 2015; 28:481-9. [PMID: 25877663 PMCID: PMC4596278 DOI: 10.1093/protein/gzv022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/27/2015] [Accepted: 03/06/2015] [Indexed: 12/14/2022] Open
Abstract
Systemic injection of granulocyte colony-stimulating factor (G-CSF) has yielded encouraging results in treating Alzheimer's Disease (AD) and other central nervous system (CNS) disorders. Making G-CSF a viable AD therapeutic will, however, require increasing G-CSF's ability to stimulate neurons within the brain. This objective could be realized by increasing transcytosis of G-CSF across the blood brain barrier (BBB). An established correlation between G-CSF receptor (G-CSFR) binding pH responsiveness and increased recycling of G-CSF to the cell exterior after endocytosis motivated development of G-CSF variants with highly pH responsive G-CSFR binding affinities. These variants will be used in future validation of our hypothesis that increased BBB transcytosis can enhance G-CSF therapeutic efficacy. Flow cytometric screening of a yeast-displayed library in which G-CSF/G-CSFR interface residues were mutated to histidine yielded a G-CSF triple His mutant (L109H/D110H/Q120H) with highly pH responsive binding affinity. This variant's KD, measured by surface plasmon resonance (SPR), increases ∼20-fold as pH decreases from 7.4 to below histidine's pKa of ∼6.0; an increase 2-fold greater than for previously reported G-CSF His mutants. Cell-free protein synthesis (CFPS) enabled expression and purification of soluble, bioactive G-CSF triple His variant protein, an outcome inaccessible via Escherichia coli inclusion body refolding. This purification and bioactivity validation will enable future identification of correlations between pH responsiveness and transcytosis in BBB cell culture model and animal experiments. Furthermore, the library screening and CFPS methods employed here could be applied to developing other pH responsive hematopoietic or neurotrophic factors for treating CNS disorders.
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Affiliation(s)
- Pete Heinzelman
- Department of Chemical, Biological and Materials Engineering, University of Oklahoma, Sarkeys Energy Center, 100 East Boyd Street, Room T-301, Norman, OK 73019, USA
| | - Jennifer A Schoborg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208-3120, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208-3120, USA
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Schröter C, Günther R, Rhiel L, Becker S, Toleikis L, Doerner A, Becker J, Schönemann A, Nasu D, Neuteboom B, Kolmar H, Hock B. A generic approach to engineer antibody pH-switches using combinatorial histidine scanning libraries and yeast display. MAbs 2015; 7:138-51. [PMID: 25523975 PMCID: PMC4622719 DOI: 10.4161/19420862.2014.985993] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
There is growing interest in the fast and robust engineering of protein pH-sensitivity that aims to reduce binding at acidic pH, compared to neutral pH. Here, we describe a novel strategy for the incorporation of pH-sensitive antigen binding functions into antibody variable domains using combinatorial histidine scanning libraries and yeast surface display. The strategy allows simultaneous screening for both, high affinity binding at pH 7.4 and pH-sensitivity, and excludes conventional negative selection steps. As proof of concept, we applied this strategy to incorporate pH-dependent antigen binding into the complementary-determining regions of adalimumab. After 3 consecutive rounds of separate heavy and light chain library screening, pH-sensitive variants could be isolated. Heavy and light chain mutations were combined, resulting in 3 full-length antibody variants that revealed sharp, reversible pH-dependent binding profiles. Dissociation rate constants at pH 6.0 increased 230- to 780-fold, while high affinity binding at pH 7.4 in the sub-nanomolar range was retained. Furthermore, binding to huFcRn and thermal stability were not affected by histidine substitutions. Overall, this study emphasizes a generalizable strategy for engineering pH-switch functions potentially applicable to a variety of antibodies and further proteins-based therapeutics.
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Affiliation(s)
- Christian Schröter
- a Institute for Organic Chemistry and Biochemistry ; Technische Universität Darmstadt ; Darmstadt , Germany
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46
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Roberts KE, Gainza P, Hallen MA, Donald BR. Fast gap-free enumeration of conformations and sequences for protein design. Proteins 2015; 83:1859-1877. [PMID: 26235965 DOI: 10.1002/prot.24870] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/14/2015] [Accepted: 07/21/2015] [Indexed: 12/12/2022]
Abstract
Despite significant successes in structure-based computational protein design in recent years, protein design algorithms must be improved to increase the biological accuracy of new designs. Protein design algorithms search through an exponential number of protein conformations, protein ensembles, and amino acid sequences in an attempt to find globally optimal structures with a desired biological function. To improve the biological accuracy of protein designs, it is necessary to increase both the amount of protein flexibility allowed during the search and the overall size of the design, while guaranteeing that the lowest-energy structures and sequences are found. DEE/A*-based algorithms are the most prevalent provable algorithms in the field of protein design and can provably enumerate a gap-free list of low-energy protein conformations, which is necessary for ensemble-based algorithms that predict protein binding. We present two classes of algorithmic improvements to the A* algorithm that greatly increase the efficiency of A*. First, we analyze the effect of ordering the expansion of mutable residue positions within the A* tree and present a dynamic residue ordering that reduces the number of A* nodes that must be visited during the search. Second, we propose new methods to improve the conformational bounds used to estimate the energies of partial conformations during the A* search. The residue ordering techniques and improved bounds can be combined for additional increases in A* efficiency. Our enhancements enable all A*-based methods to more fully search protein conformation space, which will ultimately improve the accuracy of complex biomedically relevant designs.
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Affiliation(s)
- Kyle E Roberts
- Department of Computer Science, Duke University, Durham, NC
| | - Pablo Gainza
- Department of Computer Science, Duke University, Durham, NC
| | - Mark A Hallen
- Department of Computer Science, Duke University, Durham, NC
| | - Bruce R Donald
- Department of Computer Science, Duke University, Durham, NC.,Department of Biochemistry, Duke University Medical Center, Durham, NC.,Department of Chemistry, Duke University, Durham, NC
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47
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Designing cell-targeted therapeutic proteins reveals the interplay between domain connectivity and cell binding. Biophys J 2015; 107:2456-66. [PMID: 25418314 DOI: 10.1016/j.bpj.2014.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/11/2014] [Accepted: 10/03/2014] [Indexed: 01/22/2023] Open
Abstract
The therapeutic efficacy of cytokines is often hampered by severe side effects due to their undesired binding to healthy cells. One strategy for overcoming this obstacle is to tether cytokines to antibodies or antibody fragments for targeted cell delivery. However, how to modulate the geometric configuration and relative binding affinity of the two domains for optimal activity remains an outstanding question. As a result, many antibody-cytokine complexes do not achieve the desired level of cell-targeted binding and activity. Here, we address these design issues by developing a computational model to simulate the dynamics and binding kinetics of natural and engineered fusion proteins such as antibody-cytokine complexes. To verify the model, we developed a modular system in which an antibody fragment and a cytokine are conjugated via a DNA linker that allows for programmable linker geometry and protein spatial configuration. By assembling and testing several anti-CD20 antibody fragment-interferon ? complexes, we showed that varying the linker length and cytokine binding affinity controlled the magnitude of cell-targeted signaling activation in a manner that agreed with the model predictions, which were expressed as dose-signaling response curves. The simulation results also revealed that there is a range of cytokine binding affinities that would achieve optimal therapeutic efficacy. This rapid prototyping platform will facilitate the rational design of antibody-cytokine complexes for improved therapeutic outcomes.
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Heinzelman P, Krais J, Ruben E, Pantazes R. Engineering pH responsive fibronectin domains for biomedical applications. J Biol Eng 2015; 9:6. [PMID: 26106447 PMCID: PMC4477602 DOI: 10.1186/s13036-015-0004-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/01/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Engineered antibodies with pH responsive cell surface target antigen-binding affinities that decrease at the acidic pH (5.5-5.8) within the endosomes have been found to have reduced susceptibility to degradation within the lysosomes and increased serum half-life. Such pH responsive recombinant antibodies have been developed for the treatment of cancer and cardiovascular disease. Engineered tenth type III human fibronectin (Fn3) domains are emerging as a class of target antigen-binding biopharmaceuticals that could complement or be superior to recombinant antibodies in a number of biomedical contexts. As such, there is strong motivation for demonstrating the feasibility of engineering Fn3s with pH responsive antigen binding behavior that could lead to improved Fn3 pharmacokinetics. RESULTS A yeast surface-displayed Fn3 histidine (His) mutant library screening approach yielded epidermal growth factor receptor (EGFR)-binding Fn3 domains with EGFR binding affinities that markedly decrease at endosomal pH; the first reported case of engineering Fn3s with pH responsive antigen binding. Yeast surface-displayed His mutant Fn3s, which contain either one or two His mutations, have equilibrium binding dissociation constants (KDs) that increase up to four-fold relative to wild type when pH is decreased from 7.4 to 5.5. Assays in which Fn3-displaying yeast were incubated with soluble EGFR after ligand-free incubation in respective neutral and acidic buffers showed that His mutant Fn3 pH responsiveness is due to reversible changes in Fn3 conformation and/or EGFR binding interface properties rather than irreversible unfolding. CONCLUSIONS We have established a generalizable method for efficiently constructing and screening Fn3 His mutant libraries that could enable both our laboratory and others to develop pH responsive Fn3s for use in a wide range of biomedical applications.
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Affiliation(s)
- Pete Heinzelman
- Department of Chemical, Biological & Materials Engineering, University of Oklahoma, Sarkeys Energy Center, 100 East Boyd Street, Room T-301, 73019 Norman, OK USA
| | - John Krais
- Department of Chemical, Biological & Materials Engineering, University of Oklahoma, Sarkeys Energy Center, 100 East Boyd Street, Room T-301, 73019 Norman, OK USA
| | - Eliza Ruben
- Department of Chemistry & Biochemistry, University of Oklahoma, 73019 Norman, OK USA
| | - Robert Pantazes
- Department of Chemical Engineering, University of California-Santa Barbara, 93106 Santa Barbara, CA USA
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Heinzelman P, Carlson SJ, Cox GN. Cytokine refacing effect reduces granulocyte macrophage colony-stimulating factor susceptibility to antibody neutralization. Protein Eng Des Sel 2015; 28:461-6. [PMID: 25855658 DOI: 10.1093/protein/gzv019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/26/2015] [Indexed: 11/14/2022] Open
Abstract
Crohn's Disease (CD) afflicts over half a million Americans with an annual economic impact exceeding $10 billion. Granulocyte macrophage colony-stimulating factor (GM-CSF) can increase patient immune responses against intestinal microbes that promote CD and has been effective for some patients in clinical trials. We have made important progress toward developing GM-CSF variants that could be more effective CD therapeutics by virtue of being less prone to neutralization by the endogenous GM-CSF autoantibodies that are highly expressed in CD patients. Yeast display engineering revealed mutations that increase GM-CSF variant binding affinity by up to ∼3-fold toward both GM-CSF receptor alpha and beta subunits in surface plasmon resonance experiments. Increased binding affinity did not reduce GM-CSF half-maximum effective concentration (EC50) values in conventional in vitro human leukocyte proliferation assays. Affinity-enhancing mutations did, however, promote a 'refacing effect' that imparted all five evaluated GM-CSF variants with increased in vitro bioactivity in the presence of GM-CSF-neutralizing polyclonal antisera. The most improved variant, H15L/R23L, was 6-fold more active than wild-type GM-CSF. Incorporation of additional known affinity-increasing mutations could augment the refacing effect and concomitant bioactivity improvements described here.
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Affiliation(s)
- Pete Heinzelman
- Department of Chemical, Biological & Materials Engineering, University of Oklahoma, Sarkeys Energy Center, 100 East Boyd Street, Room T-301, Norman, OK 73019, USA
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Traxlmayr MW, Lobner E, Hasenhindl C, Stadlmayr G, Oostenbrink C, Rüker F, Obinger C. Construction of pH-sensitive Her2-binding IgG1-Fc by directed evolution. Biotechnol J 2015; 9:1013-22. [PMID: 24964247 PMCID: PMC4314675 DOI: 10.1002/biot.201300483] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 05/05/2014] [Accepted: 06/23/2014] [Indexed: 01/17/2023]
Abstract
For most therapeutic proteins, a long serum half-life is desired. Studies have shown that decreased antigen binding at acidic pH can increase serum half-life. In this study, we aimed to investigate whether pH-dependent binding sites can be introduced into antigen binding crystallizable fragments of immunoglobulin G1 (Fcab). The C-terminal structural loops of an Fcab were engineered for reduced binding to the extracellular domain of human epidermal growth factor receptor 2 (Her2-ECD) at pH 6 compared to pH 7.4. A yeast-displayed Fcab-library was alternately selected for binding at pH 7.4 and non-binding at pH 6.0. Selected Fcab variants showed clear pH-dependent binding to soluble Her2-ECD (decrease in affinity at pH 6.0 compared to pH 7.4) when displayed on yeast. Additionally, some solubly expressed variants exhibited pH-dependent interactions with Her2-positive cells whereas their conformational and thermal stability was pH-independent. Interestingly, two of the three Fcabs did not contain a single histidine mutation but all of them contained variations next to histidines that already occurred in loops of the lead Fcab. The study demonstrates that yeast surface display is a valuable tool for directed evolution of pH-dependent binding sites in proteins.
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Affiliation(s)
- Michael W Traxlmayr
- Christian Doppler Laboratory for Antibody Engineering at Department of Chemistry and Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria; Department of Chemistry, Vienna Institute of BioTechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
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