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Liu HY, Sun XJ, Xiu SY, Zhang XY, Wang ZQ, Gu YL, Yi CX, Liu JY, Dai YS, Yuan X, Liao HP, Liu ZM, Pang XC, Li TC. Frizzled receptors (FZDs) in Wnt signaling: potential therapeutic targets for human cancers. Acta Pharmacol Sin 2024:10.1038/s41401-024-01270-3. [PMID: 38632318 DOI: 10.1038/s41401-024-01270-3] [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: 11/22/2023] [Accepted: 03/24/2024] [Indexed: 04/19/2024] Open
Abstract
Frizzled receptors (FZDs) are key contributors intrinsic to the Wnt signaling pathway, activation of FZDs triggering the Wnt signaling cascade is frequently observed in human tumors and intimately associated with an aggressive carcinoma phenotype. It has been shown that the abnormal expression of FZD receptors contributes to the manifestation of malignant characteristics in human tumors such as enhanced cell proliferation, metastasis, chemotherapy resistance as well as the acquisition of cancer stemness. Given the essential roles of FZD receptors in the Wnt signaling in human tumors, this review aims to consolidate the prevailing knowledge on the specific status of FZD receptors (FZD1-10) and elucidate their respective functions in tumor progression. Furthermore, we delineate the structural basis for binding of FZD and its co-receptors to Wnt, and provide a better theoretical foundation for subsequent studies on related mechanisms. Finally, we describe the existing biological classes of small molecule-based FZD inhibitors in detail in the hope that they can provide useful assistance for design and development of novel drug candidates targeted FZDs.
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Affiliation(s)
- Hui-Yu Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Peking University First Hospital, Beijing, 100034, China
| | - Xiao-Jiao Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Si-Yu Xiu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Xiang-Yu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Zhi-Qi Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yan-Lun Gu
- Department of Pharmacy, Peking University First Hospital, Beijing, 100034, China
| | - Chu-Xiao Yi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Jun-Yan Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Peking University First Hospital, Beijing, 100034, China
| | - Yu-Song Dai
- Department of Otorhinolaryngology Head and Neck Surgery, Peking University First Hospital, Beijing, 100034, China
| | - Xia Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Hua-Peng Liao
- Yizhang County People's Hospital, Chenzhou, 424200, China
| | - Zhen-Ming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
| | - Xiao-Cong Pang
- Department of Pharmacy, Peking University First Hospital, Beijing, 100034, China.
| | - Tian-Cheng Li
- Department of Otorhinolaryngology Head and Neck Surgery, Peking University First Hospital, Beijing, 100034, China.
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100034, China.
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2
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Li N, Ge Q, Guo Q, Tao Y. Identification and functional validation of FZD8-specific antibodies. Int J Biol Macromol 2024; 254:127846. [PMID: 37926311 DOI: 10.1016/j.ijbiomac.2023.127846] [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: 10/05/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
The Wnt pathway is an evolutionarily conserved pathway involved in stem cell homeostasis and tissue regeneration. Aberrant signaling in the Wnt pathway is highly associated with cancer. Developing antibodies to block overactivation of Frizzled receptors (FZDs), the main receptors in the Wnt pathway, is one of the viable options for treating cancer. However, obtaining isoform-specific antibodies is often challenging due to the high degree of homology among the ten FZDs. In this study, by using a synthetic library, we identified an antibody named pF8_AC3 that preferentially binds to FZD8. Guided by the structure of the complex of pF8_AC3 and FZD8, a second-generation targeted library was further constructed, and finally, the FZD8-specific antibody sF8_AG6 was obtained. Cell-based assays showed that these antibodies could selectively block FZD8-mediated signaling activation. Taken together, these antibodies have the potential to be developed into therapeutic drugs in the future.
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Affiliation(s)
- Na Li
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Qiangqiang Ge
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Qiong Guo
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China.
| | - Yuyong Tao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Research Center for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China.
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3
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Zhang L, Liu H. Exploring binding positions and backbone conformations of peptide ligands of proteins with a backbone-centred statistical energy function. J Comput Aided Mol Des 2023; 37:463-478. [PMID: 37498491 DOI: 10.1007/s10822-023-00518-0] [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: 04/18/2023] [Accepted: 07/05/2023] [Indexed: 07/28/2023]
Abstract
When designing peptide ligands based on the structure of a protein receptor, it can be very useful to narrow down the possible binding positions and bound conformations of the ligand without the need to choose its amino acid sequence in advance. Here, we construct and benchmark a tool for this purpose based on a recently reported statistical energy model named SCUBA (Sidechain-Unknown Backbone Arrangement) for designing protein backbones without considering specific amino acid sequences. With this tool, backbone fragments of different local conformation types are generated and optimized with SCUBA-driven stochastic simulations and simulated annealing, and then ranked and clustered to obtain representative backbone fragment poses of strong SCUBA interaction energies with the receptor. We computationally benchmarked the tool on 111 known protein-peptide complex structures. When the bound ligands are in the strand conformation, the method is able to generate backbone fragments of both low SCUBA energies and low root mean square deviations from experimental structures of peptide ligands. When the bound ligands are helices or coils, low-energy backbone fragments with binding poses similar to experimental structures have been generated for approximately 50% of benchmark cases. We have examined a number of predicted ligand-receptor complexes by atomistic molecular dynamics simulations, in which the peptide ligands have been found to stay at the predicted binding sites and to maintain their local conformations. These results suggest that promising backbone structures of peptides bound to protein receptors can be designed by identifying outstanding minima on the SCUBA-modeled backbone energy landscape.
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Affiliation(s)
- Lu Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Haiyan Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- School of Data Science, University of Science and Technology of China, Hefei, 230027, Anhui, China.
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4
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Nabhan AN, Webster JD, Adams JJ, Blazer L, Everrett C, Eidenschenk C, Arlantico A, Fleming I, Brightbill HD, Wolters PJ, Modrusan Z, Seshagiri S, Angers S, Sidhu SS, Newton K, Arron JR, Dixit VM. Targeted alveolar regeneration with Frizzled-specific agonists. Cell 2023; 186:2995-3012.e15. [PMID: 37321220 DOI: 10.1016/j.cell.2023.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 03/24/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023]
Abstract
Wnt ligands oligomerize Frizzled (Fzd) and Lrp5/6 receptors to control the specification and activity of stem cells in many species. How Wnt signaling is selectively activated in different stem cell populations, often within the same organ, is not understood. In lung alveoli, we show that distinct Wnt receptors are expressed by epithelial (Fzd5/6), endothelial (Fzd4), and stromal (Fzd1) cells. Fzd5 is uniquely required for alveolar epithelial stem cell activity, whereas fibroblasts utilize distinct Fzd receptors. Using an expanded repertoire of Fzd-Lrp agonists, we could activate canonical Wnt signaling in alveolar epithelial stem cells via either Fzd5 or, unexpectedly, non-canonical Fzd6. A Fzd5 agonist (Fzd5ag) or Fzd6ag stimulated alveolar epithelial stem cell activity and promoted survival in mice after lung injury, but only Fzd6ag promoted an alveolar fate in airway-derived progenitors. Therefore, we identify a potential strategy for promoting regeneration without exacerbating fibrosis during lung injury.
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Affiliation(s)
- Ahmad N Nabhan
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jarret J Adams
- AntlerA Therapeutics, 348 Hatch Drive, Foster City, CA 94404, USA
| | - Levi Blazer
- AntlerA Therapeutics, 348 Hatch Drive, Foster City, CA 94404, USA
| | - Christine Everrett
- Department of Molecular Discovery and Cancer Cell Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Celine Eidenschenk
- Department of Molecular Discovery and Cancer Cell Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Alexander Arlantico
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Isabel Fleming
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hans D Brightbill
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Paul J Wolters
- Department of Medicine, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | | | - Stephane Angers
- AntlerA Therapeutics, 348 Hatch Drive, Foster City, CA 94404, USA; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 1A2, Canada; Department of Biochemistry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sachdev S Sidhu
- AntlerA Therapeutics, 348 Hatch Drive, Foster City, CA 94404, USA; School of Pharmacy, University of Waterloo, Kitchener, ON N2G 1C5, Canada
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Joseph R Arron
- Department of Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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5
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Ding J, Lee SJ, Vlahos L, Yuki K, Rada CC, van Unen V, Vuppalapaty M, Chen H, Sura A, McCormick AK, Tomaske M, Alwahabi S, Nguyen H, Nowatzke W, Kim L, Kelly L, Vollrath D, Califano A, Yeh WC, Li Y, Kuo CJ. Therapeutic blood-brain barrier modulation and stroke treatment by a bioengineered FZD 4-selective WNT surrogate in mice. Nat Commun 2023; 14:2947. [PMID: 37268690 PMCID: PMC10238527 DOI: 10.1038/s41467-023-37689-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/27/2023] [Indexed: 06/04/2023] Open
Abstract
Derangements of the blood-brain barrier (BBB) or blood-retinal barrier (BRB) occur in disorders ranging from stroke, cancer, diabetic retinopathy, and Alzheimer's disease. The Norrin/FZD4/TSPAN12 pathway activates WNT/β-catenin signaling, which is essential for BBB and BRB function. However, systemic pharmacologic FZD4 stimulation is hindered by obligate palmitoylation and insolubility of native WNTs and suboptimal properties of the FZD4-selective ligand Norrin. Here, we develop L6-F4-2, a non-lipidated, FZD4-specific surrogate which significantly improves subpicomolar affinity versus native Norrin. In Norrin knockout (NdpKO) mice, L6-F4-2 not only potently reverses neonatal retinal angiogenesis deficits, but also restores BRB and BBB function. In adult C57Bl/6J mice, post-stroke systemic delivery of L6-F4-2 strongly reduces BBB permeability, infarction, and edema, while improving neurologic score and capillary pericyte coverage. Our findings reveal systemic efficacy of a bioengineered FZD4-selective WNT surrogate during ischemic BBB dysfunction, with potential applicability to adult CNS disorders characterized by an aberrant blood-brain barrier.
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Affiliation(s)
- Jie Ding
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sung-Jin Lee
- Surrozen, Inc. South San Francisco, South San Francisco, CA, 94080, USA
| | - Lukas Vlahos
- Department of Systems Biology, Columbia University, Columbia, NY, 10032, USA
| | - Kanako Yuki
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Cara C Rada
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Vincent van Unen
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Hui Chen
- Surrozen, Inc. South San Francisco, South San Francisco, CA, 94080, USA
| | - Asmiti Sura
- Surrozen, Inc. South San Francisco, South San Francisco, CA, 94080, USA
| | - Aaron K McCormick
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Madeline Tomaske
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Samira Alwahabi
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Huy Nguyen
- Surrozen, Inc. South San Francisco, South San Francisco, CA, 94080, USA
| | - William Nowatzke
- Surrozen, Inc. South San Francisco, South San Francisco, CA, 94080, USA
| | - Lily Kim
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lisa Kelly
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Douglas Vollrath
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, Columbia, NY, 10032, USA
| | - Wen-Chen Yeh
- Surrozen, Inc. South San Francisco, South San Francisco, CA, 94080, USA
| | - Yang Li
- Surrozen, Inc. South San Francisco, South San Francisco, CA, 94080, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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6
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Gainza P, Wehrle S, Van Hall-Beauvais A, Marchand A, Scheck A, Harteveld Z, Buckley S, Ni D, Tan S, Sverrisson F, Goverde C, Turelli P, Raclot C, Teslenko A, Pacesa M, Rosset S, Georgeon S, Marsden J, Petruzzella A, Liu K, Xu Z, Chai Y, Han P, Gao GF, Oricchio E, Fierz B, Trono D, Stahlberg H, Bronstein M, Correia BE. De novo design of protein interactions with learned surface fingerprints. Nature 2023; 617:176-184. [PMID: 37100904 PMCID: PMC10131520 DOI: 10.1038/s41586-023-05993-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 03/21/2023] [Indexed: 04/28/2023]
Abstract
Physical interactions between proteins are essential for most biological processes governing life1. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This knowledge gap has been a major obstacle for the comprehensive understanding of cellular protein-protein interaction networks and for the de novo design of protein binders that are crucial for synthetic biology and translational applications2-9. Here we use a geometric deep-learning framework operating on protein surfaces that generates fingerprints to describe geometric and chemical features that are critical to drive protein-protein interactions10. We hypothesized that these fingerprints capture the key aspects of molecular recognition that represent a new paradigm in the computational design of novel protein interactions. As a proof of principle, we computationally designed several de novo protein binders to engage four protein targets: SARS-CoV-2 spike, PD-1, PD-L1 and CTLA-4. Several designs were experimentally optimized, whereas others were generated purely in silico, reaching nanomolar affinity with structural and mutational characterization showing highly accurate predictions. Overall, our surface-centric approach captures the physical and chemical determinants of molecular recognition, enabling an approach for the de novo design of protein interactions and, more broadly, of artificial proteins with function.
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Affiliation(s)
- Pablo Gainza
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Monte Rosa Therapeutics, Basel, Switzerland
| | - Sarah Wehrle
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandra Van Hall-Beauvais
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Anthony Marchand
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Scheck
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Zander Harteveld
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stephen Buckley
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Science, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Shuguang Tan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Freyr Sverrisson
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Casper Goverde
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Priscilla Turelli
- Laboratory of Virology and Genetics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Charlène Raclot
- Laboratory of Virology and Genetics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandra Teslenko
- Laboratory of Biophysical Chemistry of Macromolecules, School of Basic Sciences, Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stéphane Rosset
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jane Marsden
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Aaron Petruzzella
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, School of Basic Sciences, Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Didier Trono
- Laboratory of Virology and Genetics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Science, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | | | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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7
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Siepe DH, Picton LK, Garcia KC. Receptor Elimination by E3 Ubiquitin Ligase Recruitment (REULR): A Targeted Protein Degradation Toolbox. ACS Synth Biol 2023; 12:1081-1093. [PMID: 37011906 PMCID: PMC10127277 DOI: 10.1021/acssynbio.2c00587] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Indexed: 04/05/2023]
Abstract
In recent years, targeted protein degradation (TPD) of plasma membrane proteins by hijacking the ubiquitin proteasome system (UPS) or the lysosomal pathway has emerged as a novel therapeutic avenue in drug development to address and inhibit canonically difficult targets. While TPD strategies have been successful in targeting cell surface receptors, these approaches are limited by the availability of suitable binders to generate heterobifunctional molecules. Here, we present the development of a nanobody (VHH)-based degradation toolbox termed REULR (Receptor Elimination by E3 Ubiquitin Ligase Recruitment). We generated human and mouse cross-reactive nanobodies against five transmembrane PA-TM-RING-type E3 ubiquitin ligases (RNF128, RNF130, RNF167, RNF43, and ZNRF3), covering a broad range and selectivity of tissue expression, with which we characterized the expression in human and mouse cell lines and immune cells (PBMCs). We demonstrate that heterobifunctional REULR molecules can enforce transmembrane E3 ligase interactions with a variety of disease-relevant target receptors (EGFR, EPOR, and PD-1) by induced proximity, resulting in effective membrane clearance of the target receptor at varying levels. In addition, we designed E3 ligase self-degrading molecules, "fratricide" REULRs (RNF128, RNF130, RENF167, RNF43, and ZNRF3), that allow downregulation of one or several E3 ligases from the cell surface and consequently modulate receptor signaling strength. REULR molecules represent a VHH-based modular and versatile "mix and match" targeting strategy for the facile modulation of cell surface proteins by induced proximity to transmembrane PA-TM-RING E3 ligases.
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Affiliation(s)
- Dirk H. Siepe
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
| | - Lora K. Picton
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
| | - K. Christopher Garcia
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Howard
Hughes Medical Institute, Stanford University
School of Medicine, Stanford, California 94305, United States
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8
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O'Brien S, Chidiac R, Angers S. Modulation of Wnt-β-catenin signaling with antibodies: therapeutic opportunities and challenges. Trends Pharmacol Sci 2023; 44:354-365. [PMID: 37085400 DOI: 10.1016/j.tips.2023.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/23/2023]
Abstract
Since the recognition that mutations in components of the Wnt-β-catenin pathway underlie some human cancers, considerable attention has been dedicated to developing therapeutic modalities to block its activity. Despite numerous efforts, no drug directly inhibiting Wnt signaling is currently clinically available. Conversely, activating the Wnt pathway in a specific manner has recently been made possible with new molecules mimicking the activity of Wnt proteins, thus offering new possibilities for controlling tissue stem cell activity and for the rational treatment of various degenerative conditions. We describe the landscape of antibody modalities that modulate the Wnt-β-catenin pathway, and detail the advances and challenges in both cancer and regenerative medicine drug development.
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Affiliation(s)
- Siobhan O'Brien
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Rony Chidiac
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Stephane Angers
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
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9
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Ge Q, Teng M, Li X, Guo Q, Tao Y. An epitope-directed selection strategy facilitating the identification of Frizzled receptor selective antibodies. Structure 2023; 31:33-43.e5. [PMID: 36513066 DOI: 10.1016/j.str.2022.11.009] [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: 04/01/2022] [Revised: 09/27/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022]
Abstract
The lack of incorporating epitope information into the selection process makes the conventional antibody screening method less effective in identifying antibodies with desired functions. Here, we developed an epitope-directed antibody selection method by designing a directed library favoring the target epitope and a precise "counter" antigen for clearing irrelevant binders in the library. With this method, we successfully isolated an antibody, pF7_A5, that targets the less conserved region on the FZD2/7 CRD as designed. Guided by the structure of pF7_A5-FZD2CRD, a further round of evolution was conducted together with the "counter" antigen selection strategy, and ultimately, an FZD2-specific antibody and an FZD7-preferred antibody were obtained. Because of targeting the predefined functional site, all these antibodies exhibited the expected modulatory activity on the Wnt pathway. Together, the method developed here will be useful in antibody drug discovery, and the identified FZD antibodies will have clinical potential in FZD-related cancer therapy.
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Affiliation(s)
- Qiangqiang Ge
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China
| | - Maikun Teng
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China.
| | - Xu Li
- Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China.
| | - Qiong Guo
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China.
| | - Yuyong Tao
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, P.R. China; Joint Laboratory of Innovation in Life Sciences University of Science and Technology of China (USTC) and Changchun Zhuoyi Biological Co. Ltd., 130616 Changchun, P.R. China.
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10
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Park JS, Choi J, Cao L, Mohanty J, Suzuki Y, Park A, Baker D, Schlessinger J, Lee S. Isoform-specific inhibition of FGFR signaling achieved by a de-novo-designed mini-protein. Cell Rep 2022; 41:111545. [PMID: 36288716 PMCID: PMC9636537 DOI: 10.1016/j.celrep.2022.111545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/16/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022] Open
Abstract
Cellular signaling by fibroblast growth factor receptors (FGFRs) is a highly regulated process mediated by specific interactions between distinct subsets of fibroblast growth factor (FGF) ligands and two FGFR isoforms generated by alternative splicing: an epithelial b- and mesenchymal c-isoforms. Here, we investigate the properties of a mini-protein, mb7, developed by an in silico design strategy to bind to the ligand-binding region of FGFR2. We describe structural, biophysical, and cellular analyses demonstrating that mb7 binds with high affinity to the c-isoforms of FGFR, resulting in inhibition of cellular signaling induced by a subset of FGFs that preferentially activate c-isoforms of FGFR. Notably, as mb7 blocks interaction between FGFR with Klotho proteins, it functions as an antagonist of the metabolic hormones FGF19 and FGF21, providing mechanistic insights and strategies for the development of therapeutics for diseases driven by aberrantly activated FGFRs. Park et al. show that a de-novo-designed mini-protein, mb7, can specifically recognize c-isoforms of FGFRs. By masking the regions of FGFR that are critical for the FGFR activation, mb7 can potently inhibit cellular signaling by a subset of FGFs that preferentially activate FGFR c-isoform signaling.
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11
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Marchand A, Van Hall-Beauvais AK, Correia BE. Computational design of novel protein–protein interactions – An overview on methodological approaches and applications. Curr Opin Struct Biol 2022; 74:102370. [DOI: 10.1016/j.sbi.2022.102370] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022]
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12
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Xie L, Fletcher RB, Bhatia D, Shah D, Phipps J, Deshmukh S, Zhang H, Ye J, Lee S, Le L, Newman M, Chen H, Sura A, Gupta S, Sanman LE, Yang F, Meng W, Baribault H, Vanhove GF, Yeh WC, Li Y, Lu C. Robust Colonic Epithelial Regeneration and Amelioration of Colitis via FZD-Specific Activation of Wnt Signaling. Cell Mol Gastroenterol Hepatol 2022; 14:435-464. [PMID: 35569814 PMCID: PMC9305022 DOI: 10.1016/j.jcmgh.2022.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Current management of inflammatory bowel disease leaves a clear unmet need to treat the severe epithelial damage. Modulation of Wnt signaling might present an opportunity to achieve histological remission and mucosal healing when treating IBD. Exogenous R-spondin, which amplifies Wnt signals by maintaining cell surface expression of Frizzled (Fzd) and low-density lipoprotein receptor-related protein receptors, not only helps repair intestine epithelial damage, but also induces hyperplasia of normal epithelium. Wnt signaling may also be modulated with the recently developed Wnt mimetics, recombinant antibody-based molecules mimicking endogenous Wnts. METHODS We first compared the epithelial healing effects of RSPO2 and a Wnt mimetic with broad Fzd specificity in an acute dextran sulfate sodium mouse colitis model. Guided by Fzd expression patterns in the colon epithelium, we also examined the effects of Wnt mimetics with subfamily Fzd specificities. RESULTS In the DSS model, Wnt mimetics repaired damaged colon epithelium and reduced disease activity and inflammation and had no apparent effect on uninjured tissue. We further identified that the FZD5/8 and LRP6 receptor-specific Wnt mimetic, SZN-1326-p, was associated with the robust repair effect. Through a range of approaches including single-cell transcriptome analyses, we demonstrated that SZN-1326-p directly impacted epithelial cells, driving transient expansion of stem and progenitor cells, promoting differentiation of epithelial cells, histologically restoring the damaged epithelium, and secondarily to epithelial repair, reducing inflammation. CONCLUSIONS It is feasible to design Wnt mimetics such as SZN-1326-p that impact damaged intestine epithelium specifically and restore its physiological functions, an approach that holds promise for treating epithelial damage in inflammatory bowel disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Chenggang Lu
- Correspondence Address correspondence to: Chenggang Lu, PhD, Surrozen, Inc., 171 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080.
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13
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Swanson S, Sivaraman V, Grigoryan G, Keating AE. Tertiary motifs as building blocks for the design of protein‐binding peptides. Protein Sci 2022; 31:e4322. [PMID: 35634780 PMCID: PMC9088223 DOI: 10.1002/pro.4322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Sebastian Swanson
- Department of Biology Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Venkatesh Sivaraman
- Department of Biology Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Gevorg Grigoryan
- Department of Computer Science Dartmouth College Hanover New Hampshire USA
| | - Amy E. Keating
- Department of Biology Massachusetts Institute of Technology Cambridge Massachusetts USA
- Department of Biological Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
- Koch Center for Integrative Cancer Research Massachusetts Institute of Technology Cambridge Massachusetts USA
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14
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Abstract
The Wnt pathway is central to a host of developmental and disease-related processes. The remarkable conservation of this intercellular signaling cascade throughout metazoan lineages indicates that it coevolved with multicellularity to regulate the generation and spatial arrangement of distinct cell types. By regulating cell fate specification, mitotic activity, and cell polarity, Wnt signaling orchestrates development and tissue homeostasis, and its dysregulation is implicated in developmental defects, cancer, and degenerative disorders. We review advances in our understanding of this key pathway, from Wnt protein production and secretion to relay of the signal in the cytoplasm of the receiving cell. We discuss the evolutionary history of this pathway as well as endogenous and synthetic modulators of its activity. Finally, we highlight remaining gaps in our knowledge of Wnt signal transduction and avenues for future research. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ellen Youngsoo Rim
- Howard Hughes Medical Institute, Department of Developmental Biology, and Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, California, USA;
| | - Hans Clevers
- Hubrecht Institute and Oncode Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
| | - Roel Nusse
- Howard Hughes Medical Institute, Department of Developmental Biology, and Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, California, USA;
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15
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Larasati Y, Boudou C, Koval A, Katanaev VL. Unlocking the Wnt pathway: Therapeutic potential of selective targeting FZD 7 in cancer. Drug Discov Today 2021; 27:777-792. [PMID: 34915171 DOI: 10.1016/j.drudis.2021.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/09/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023]
Abstract
The Wnt signaling is of paramount pathophysiological importance. Despite showing promising anticancer activities in pre-clinical studies, current Wnt pathway inhibitors face complications in clinical trials resulting from on-target toxicity. Hence, the targeting of pathway component(s) that are essential for cancer but dispensable for normal physiology is key to the development of a safe Wnt signaling inhibitor. Frizzled7 (FZD7) is a Wnt pathway receptor that is redundant in healthy tissues but crucial in various cancers. FZD7 modulates diverse aspects of carcinogenesis, including cancer growth, metastasis, maintenance of cancer stem cells, and chemoresistance. In this review, we describe state-of-the-art knowledge of the functions of FZD7 in carcinogenesis and adult tissue homeostasis. Next, we overview the development of small molecules and biomolecules that target FZD7. Finally, we discuss challenges and possibilities in developing FZD7-selective antagonists.
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Affiliation(s)
- Yonika Larasati
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Cédric Boudou
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Alexey Koval
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Vladimir L Katanaev
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; School of Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia.
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16
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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17
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Abstract
Duplication and divergence is a major mechanism by which new proteins and functions emerge in biology. Consequently, most organisms, in all domains of life, have genomes that encode large paralogous families of proteins. For recently duplicated pathways to acquire different, independent functions, the two paralogs must acquire mutations that effectively insulate them from one another. For instance, paralogous signaling proteins must acquire mutations that endow them with different interaction specificities such that they can participate in different signaling pathways without disruptive cross-talk. Although duplicated genes undoubtedly shape each other's evolution as they diverge and attain new functions, it is less clear how other paralogs impact or constrain gene duplication. Does the establishment of a new pathway by duplication and divergence require the system-wide optimization of all paralogs? The answer has profound implications for molecular evolution and our ability to engineer biological systems. Here, we discuss models, experiments, and approaches for tackling this question, and for understanding how new proteins and pathways are born.
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Affiliation(s)
- Conor J McClune
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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18
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The structural biology of canonical Wnt signalling. Biochem Soc Trans 2021; 48:1765-1780. [PMID: 32725184 PMCID: PMC7458405 DOI: 10.1042/bst20200243] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022]
Abstract
The Wnt signalling pathways are of great importance in embryonic development and oncogenesis. Canonical and non-canonical Wnt signalling pathways are known, with the canonical (or β-catenin dependent) pathway being perhaps the best studied of these. While structural knowledge of proteins and interactions involved in canonical Wnt signalling has accumulated over the past 20 years, the pace of discovery has increased in recent years, with the structures of several key proteins and assemblies in the pathway being released. In this review, we provide a brief overview of canonical Wnt signalling, followed by a comprehensive overview of currently available X-ray, NMR and cryoEM data elaborating the structures of proteins and interactions involved in canonical Wnt signalling. While the volume of structures available is considerable, numerous gaps in knowledge remain, particularly a comprehensive understanding of the assembly of large multiprotein complexes mediating key aspects of pathway, as well as understanding the structure and activation of membrane receptors in the pathway. Nonetheless, the presently available data affords considerable opportunities for structure-based drug design efforts targeting canonical Wnt signalling.
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19
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Abstract
The WNT/β-catenin signalling pathway is a rich and complex network of cellular proteins that orchestrates diverse short-range cell-to-cell communication in metazoans and is essential for both embryonic development and adult homeostasis. Due to its fundamental importance in controlling cell behaviour at multiple levels, its deregulation is associated with a wide range of diseases in humans and identification of drugs targeting the pathway has attracted strong interest in the pharmaceutical sector. Transduction of WNT signals across the plasma membrane of cells involves a staggering degree of complexity and variety with respect to ligand-receptor, receptor-receptor and receptor-co-receptor interactions (Niehrs, Nat Rev Mol Cell Biol 13:767-779, 2012). Although the low-density-lipoprotein-receptor-related-protein (LRP) family is best known for its role in binding and endocytosis of lipoproteins, specific members appear to have additional roles in cellular communication. Indeed, for WNT/β-catenin signalling one apparently universal requirement is the presence of either LRP5 or LRP6 in combination with one of the ten Frizzled (FZD) WNT receptors (FZD1-10). In the 20 years since their discovery as WNT/FZD co-receptors, research on the LRP family has contributed greatly to our understanding of WNT signalling and LRPs have emerged as central players in WNT/β-catenin signalling. LRP5/6 are highly similar and represent the least redundant class of WNT receptor that transduce WNT/β-catenin signalling from a wide range of different WNT and FZD subtypes. This apparent simplicity however belies the complex arrangement of binding sites in the extracellular domain (ECD) of LRP5/6, which regulate interaction not only with WNTs but also with several inhibitors of WNT signalling. This chapter provides a historical overview, chronologically charting this remarkable progress in the field during the last 20 years of research on LRPs and their role in WNT/-catenin signalling. A more focused overview of the structural, functional and mechanistic aspects of LRP biology is also provided, together with the implications this has for pharmacological targeting of this notoriously intractable pathway.
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Affiliation(s)
- Gary Davidson
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBSC-FMS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
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20
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Sonavane PR, Willert K. Controlling Wnt Signaling Specificity and Implications for Targeting WNTs Pharmacologically. Handb Exp Pharmacol 2021; 269:3-28. [PMID: 34463853 DOI: 10.1007/164_2021_529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Wnt signaling is critical for proper development of the embryo and for tissue homeostasis in the adult. Activation of this signaling cascade is initiated by binding of the secreted Wnts to their receptors. With the mammalian genome encoding multiple Wnts and Wnt receptors, a longstanding question in the field has been how Wnt-receptor specificities are achieved. Emerging from these studies is a picture of exquisite control over Wnt protein production, secretion, distribution, and receptor interactions, culminating in activation of downstream signaling cascades that control a myriad of biological processes. Here we discuss mechanisms by which Wnt protein activities are tuned and illustrate how the multiple layers of regulation can be leveraged for therapeutic interventions in disease.
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Affiliation(s)
- Pooja R Sonavane
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Karl Willert
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
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21
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Gumber D, Do M, Suresh Kumar N, Sonavane PR, Wu CCN, Cruz LS, Grainger S, Carson D, Gaasterland T, Willert K. Selective activation of FZD7 promotes mesendodermal differentiation of human pluripotent stem cells. eLife 2020; 9:e63060. [PMID: 33331818 PMCID: PMC7759383 DOI: 10.7554/elife.63060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/16/2020] [Indexed: 01/01/2023] Open
Abstract
WNT proteins are secreted symmetry breaking signals that interact with cell surface receptors of the FZD family to regulate a multitude of developmental processes. Studying selectivity between WNTs and FZDs has been hampered by the paucity of purified WNT proteins and by their apparent non-selective interactions with the FZD receptors. Here, we describe an engineered protein, called F7L6, comprised of antibody-derived single-chain variable fragments, that selectively binds to human FZD7 and the co-receptor LRP6. F7L6 potently activates WNT/β-catenin signaling in a manner similar to Wnt3a. In contrast to Wnt3a, F7L6 engages only FZD7 and none of the other FZD proteins. Treatment of human pluripotent stem (hPS) cells with F7L6 initiates transcriptional programs similar to those observed during primitive streak formation and subsequent gastrulation in the mammalian embryo. This demonstrates that selective engagement and activation of FZD7 signaling is sufficient to promote mesendodermal differentiation of hPS cells.
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Affiliation(s)
- Diana Gumber
- Department of Cellular & Molecular Medicine, University of California San DiegoSan DiegoUnited States
| | - Myan Do
- Department of Cellular & Molecular Medicine, University of California San DiegoSan DiegoUnited States
| | - Neya Suresh Kumar
- Department of Cellular & Molecular Medicine, University of California San DiegoSan DiegoUnited States
| | - Pooja R Sonavane
- Department of Cellular & Molecular Medicine, University of California San DiegoSan DiegoUnited States
| | - Christina C N Wu
- Department of Medicine, University of California San DiegoSan DiegoUnited States
| | - Luisjesus S Cruz
- Department of Biology, San Diego State UniversitySan DiegoUnited States
| | | | - Dennis Carson
- Department of Medicine, University of California San DiegoSan DiegoUnited States
| | - Terry Gaasterland
- University of California San Diego and Scripps Institution of Oceanography, Scripps Genome CenterLa JollaUnited States
| | - Karl Willert
- Department of Cellular & Molecular Medicine, University of California San DiegoSan DiegoUnited States
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22
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Substrate Specificity and Structural Modeling of Human Carboxypeptidase Z: A Unique Protease with a Frizzled-Like Domain. Int J Mol Sci 2020; 21:ijms21228687. [PMID: 33217972 PMCID: PMC7698808 DOI: 10.3390/ijms21228687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/29/2022] Open
Abstract
Metallocarboxypeptidase Z (CPZ) is a secreted enzyme that is distinguished from all other members of the M14 metallocarboxypeptidase family by the presence of an N-terminal cysteine-rich Frizzled-like (Fz) domain that binds Wnt proteins. Here, we present a comprehensive analysis of the enzymatic properties and substrate specificity of human CPZ. To investigate the enzymatic properties, we employed dansylated peptide substrates. For substrate specificity profiling, we generated two different large peptide libraries and employed isotopic labeling and quantitative mass spectrometry to study the substrate preference of this enzyme. Our findings revealed that CPZ has a strict requirement for substrates with C-terminal Arg or Lys at the P1′ position. For the P1 position, CPZ was found to display specificity towards substrates with basic, small hydrophobic, or polar uncharged side chains. Deletion of the Fz domain did not affect CPZ activity as a carboxypeptidase. Finally, we modeled the structure of the Fz and catalytic domains of CPZ. Taken together, these studies provide the molecular elucidation of substrate recognition and specificity of the CPZ catalytic domain, as well as important insights into how the Fz domain binds Wnt proteins to modulate their functions.
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23
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Glasgow A, Glasgow J, Limonta D, Solomon P, Lui I, Zhang Y, Nix MA, Rettko NJ, Zha S, Yamin R, Kao K, Rosenberg OS, Ravetch JV, Wiita AP, Leung KK, Lim SA, Zhou XX, Hobman TC, Kortemme T, Wells JA. Engineered ACE2 receptor traps potently neutralize SARS-CoV-2. Proc Natl Acad Sci U S A 2020; 117:28046-28055. [PMID: 33093202 PMCID: PMC7668070 DOI: 10.1073/pnas.2016093117] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
An essential mechanism for severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here, we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2-RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest-affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human immunoglobulin crystallizable fragment (Fc) domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2-pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50s) in the 10- to 100-ng/mL range. Engineered ACE2 receptor traps offer a promising route to fighting infections by SARS-CoV-2 and other ACE2-using coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be predesigned for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies isolated from convalescent patients.
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Affiliation(s)
- Anum Glasgow
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Jeff Glasgow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Daniel Limonta
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Paige Solomon
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Yang Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Matthew A Nix
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
| | - Nicholas J Rettko
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Shoshana Zha
- Department of Medicine, University of California, San Francisco, CA 94143
| | - Rachel Yamin
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY 10065
| | - Kevin Kao
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY 10065
| | - Oren S Rosenberg
- Department of Medicine, University of California, San Francisco, CA 94143
| | - Jeffrey V Ravetch
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY 10065
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Shion A Lim
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Xin X Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Tom C Hobman
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
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24
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Abstract
In this issue of Cell Chemical Biology, Chen et al. (2020) present an antibody-based platform to generate Wnt agonists, offering multiple design principles for systematic investigation of Wnt activation. This study lays the groundwork to develop potent Wnt agonists for applications in regenerative medicine.
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Affiliation(s)
- Simon Hansen
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, USA.
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25
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Miao Y, Ha A, de Lau W, Yuki K, Santos AJM, You C, Geurts MH, Puschhof J, Pleguezuelos-Manzano C, Peng WC, Senlice R, Piani C, Buikema JW, Gbenedio OM, Vallon M, Yuan J, de Haan S, Hemrika W, Rösch K, Dang LT, Baker D, Ott M, Depeille P, Wu SM, Drost J, Nusse R, Roose JP, Piehler J, Boj SF, Janda CY, Clevers H, Kuo CJ, Garcia KC. Next-Generation Surrogate Wnts Support Organoid Growth and Deconvolute Frizzled Pleiotropy In Vivo. Cell Stem Cell 2020; 27:840-851.e6. [PMID: 32818433 DOI: 10.1016/j.stem.2020.07.020] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/02/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022]
Abstract
Modulation of Wnt signaling has untapped potential in regenerative medicine due to its essential functions in stem cell homeostasis. However, Wnt lipidation and Wnt-Frizzled (Fzd) cross-reactivity have hindered translational Wnt applications. Here, we designed and engineered water-soluble, Fzd subtype-specific "next-generation surrogate" (NGS) Wnts that hetero-dimerize Fzd and Lrp6. NGS Wnt supports long-term expansion of multiple different types of organoids, including kidney, colon, hepatocyte, ovarian, and breast. NGS Wnts are superior to Wnt3a conditioned media in organoid expansion and single-cell organoid outgrowth. Administration of Fzd subtype-specific NGS Wnt in vivo reveals that adult intestinal crypt proliferation can be promoted by agonism of Fzd5 and/or Fzd8 receptors, while a broad spectrum of Fzd receptors can induce liver zonation. Thus, NGS Wnts offer a unified organoid expansion protocol and a laboratory "tool kit" for dissecting the functions of Fzd subtypes in stem cell biology.
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Affiliation(s)
- Yi Miao
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Ha
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wim de Lau
- Oncode Institute, Hubrecht Institute, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Kanako Yuki
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - António J M Santos
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Changjiang You
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Maarten H Geurts
- Oncode Institute, Hubrecht Institute, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Jens Puschhof
- Oncode Institute, Hubrecht Institute, University Medical Centre Utrecht, Utrecht, the Netherlands
| | | | - Weng Chuan Peng
- Howard Hughes Medical Institute, Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ramazan Senlice
- Foundation Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Carol Piani
- Foundation Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Jan W Buikema
- Department of Cardiology, University Medical Center Utrecht & Utrecht Regenerative Medicine Center, Utrecht University, 3508 GA Utrecht, the Netherlands
| | | | - Mario Vallon
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jenny Yuan
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sanne de Haan
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Wieger Hemrika
- U-Protein Express BV, Yalelaan 62, 3584 CM Utrecht, the Netherlands
| | - Kathrin Rösch
- Gladstone Institutes and Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Luke T Dang
- Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - David Baker
- Department of Biochemistry, Institute for Protein Design and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Melanie Ott
- Gladstone Institutes and Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Philippe Depeille
- Department of Cardiology, University Medical Center Utrecht & Utrecht Regenerative Medicine Center, Utrecht University, 3508 GA Utrecht, the Netherlands
| | - Sean M Wu
- Division of Cardiovascular Medicine, Department of Medicine, Cardiovascular Institute and Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jarno Drost
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Roeland Nusse
- Howard Hughes Medical Institute, Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob Piehler
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Sylvia F Boj
- Foundation Hubrecht Organoid Technology (HUB), Utrecht, the Netherlands
| | - Claudia Y Janda
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, University Medical Centre Utrecht, Utrecht, the Netherlands; Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Department of Structural Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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26
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Tsutsumi N, Mukherjee S, Waghray D, Janda CY, Jude KM, Miao Y, Burg JS, Aduri NG, Kossiakoff AA, Gati C, Garcia KC. Structure of human Frizzled5 by fiducial-assisted cryo-EM supports a heterodimeric mechanism of canonical Wnt signaling. eLife 2020; 9:e58464. [PMID: 32762848 PMCID: PMC7442489 DOI: 10.7554/elife.58464] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/06/2020] [Indexed: 01/19/2023] Open
Abstract
Frizzleds (Fzd) are the primary receptors for Wnt morphogens, which are essential regulators of stem cell biology, yet the structural basis of Wnt signaling through Fzd remains poorly understood. Here we report the structure of an unliganded human Fzd5 determined by single-particle cryo-EM at 3.7 Å resolution, with the aid of an antibody chaperone acting as a fiducial marker. We also analyzed the topology of low-resolution XWnt8/Fzd5 complex particles, which revealed extreme flexibility between the Wnt/Fzd-CRD and the Fzd-TM regions. Analysis of Wnt/β-catenin signaling in response to Wnt3a versus a 'surrogate agonist' that cross-links Fzd to LRP6, revealed identical structure-activity relationships. Thus, canonical Wnt/β-catenin signaling appears to be principally reliant on ligand-induced Fzd/LRP6 heterodimerization, versus the allosteric mechanisms seen in structurally analogous class A G protein-coupled receptors, and Smoothened. These findings deepen our mechanistic understanding of Wnt signal transduction, and have implications for harnessing Wnt agonism in regenerative medicine.
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Affiliation(s)
- Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Deepa Waghray
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
| | - Claudia Y Janda
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Princess Máxima Center for Pediatric OncologyUtrechtNetherlands
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
| | - Yi Miao
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
| | - John S Burg
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
| | - Nanda Gowtham Aduri
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- SLAC National Accelerator Laboratory, Bioscience DivisionMenlo ParkUnited States
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Cornelius Gati
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- SLAC National Accelerator Laboratory, Bioscience DivisionMenlo ParkUnited States
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
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27
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Glasgow A, Glasgow J, Limonta D, Solomon P, Lui I, Zhang Y, Nix MA, Rettko NJ, Lim SA, Zha S, Yamin R, Kao K, Rosenberg OS, Ravetch JV, Wiita AP, Leung KK, Zhou XX, Hobman TC, Kortemme T, Wells JA. Engineered ACE2 receptor traps potently neutralize SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.31.231746. [PMID: 32766586 PMCID: PMC7402043 DOI: 10.1101/2020.07.31.231746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An essential mechanism for SARS-CoV-1 and -2 infection begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2-RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human Fc domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2 pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50) in the 10-100 ng/ml range. Engineered ACE2 receptor traps offer a promising route to fighting infections by SARS-CoV-2 and other ACE2-utilizing coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be predesigned for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies isolated or generated from convalescent patients.
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Affiliation(s)
- Anum Glasgow
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, CA
| | - Jeff Glasgow
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Daniel Limonta
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Paige Solomon
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Yang Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, CA
| | - Matthew A. Nix
- Department of Laboratory Medicine, University of California at San Francisco, CA
| | - Nicholas J. Rettko
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Shion A. Lim
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Shoshana Zha
- Department of Medicine, University of California at San Francisco, CA
| | - Rachel Yamin
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY
| | - Kevin Kao
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY
| | - Oren S. Rosenberg
- Department of Medicine, University of California at San Francisco, CA
| | - Jeffrey V. Ravetch
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY
| | - Arun P. Wiita
- Department of Laboratory Medicine, University of California at San Francisco, CA
| | - Kevin K. Leung
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Xin X. Zhou
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
| | - Tom C. Hobman
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
- Department of Cell Biology, University of Alberta, Edmonton, Canada
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Canada
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, CA
| | - James A. Wells
- Department of Pharmaceutical Chemistry, University of California at San Francisco, CA
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, CA
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28
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Chen H, Lu C, Ouyang B, Zhang H, Huang Z, Bhatia D, Lee SJ, Shah D, Sura A, Yeh WC, Li Y. Development of Potent, Selective Surrogate WNT Molecules and Their Application in Defining Frizzled Requirements. Cell Chem Biol 2020; 27:598-609.e4. [PMID: 32220333 DOI: 10.1016/j.chembiol.2020.02.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/10/2020] [Accepted: 02/27/2020] [Indexed: 01/20/2023]
Abstract
WNTs regulate myriad biological processes during embryonic development and are key regulators of stem cell function, tissue homeostasis, and injury repair in adults. The creation of WNT-based therapies has been hampered by challenges in developing soluble, potent, and selective WNT molecules. Soluble WNT surrogates have been reported, but they demonstrate relatively weak WNT signaling activity. Here, we describe a platform for potent, selective WNT surrogate generation. We identify multivalent binding to Frizzleds (FZDs) and low-density lipoprotein receptor-related proteins (LRPs) to be a requirement for maximal WNT/β-catenin activation. Furthermore, we show that recruitment of two different FZDs together with LRP causes efficient signaling. Surrogate WNT targeting either FZD1,2,7 or FZD5,8 induces expansive growth of intestinal organoids. This flexible WNT surrogate platform yields potent agonists with any desired receptor specificity and will be useful for research and therapeutic applications for tissue regeneration.
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Affiliation(s)
- Hui Chen
- Surrozen Inc., 171 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA
| | - Chenggang Lu
- Surrozen Inc., 171 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA
| | - Brian Ouyang
- Surrozen Inc., 171 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA
| | - Haili Zhang
- Surrozen Inc., 171 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA
| | - Zhong Huang
- Surrozen Inc., 171 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA
| | - Diksha Bhatia
- Surrozen Inc., 171 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA
| | - Sung-Jin Lee
- Surrozen Inc., 171 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA
| | - Darshini Shah
- Surrozen Inc., 171 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA
| | - Asmiti Sura
- Surrozen Inc., 171 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA
| | - Wen-Chen Yeh
- Surrozen Inc., 171 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA
| | - Yang Li
- Surrozen Inc., 171 Oyster Point Boulevard, Suite 400, South San Francisco, CA 94080, USA.
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29
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Zhao Y, Ren J, Hillier J, Lu W, Jones EY. Antiepileptic Drug Carbamazepine Binds to a Novel Pocket on the Wnt Receptor Frizzled-8. J Med Chem 2020; 63:3252-3260. [PMID: 32049522 PMCID: PMC7104226 DOI: 10.1021/acs.jmedchem.9b02020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 01/07/2023]
Abstract
Misregulation of Wnt signaling is common in human cancer. The development of small molecule inhibitors against the Wnt receptor, frizzled (FZD), may have potential in cancer therapy. During small molecule screens, we observed binding of carbamazepine to the cysteine-rich domain (CRD) of the Wnt receptor FZD8 using surface plasmon resonance (SPR). Cellular functional assays demonstrated that carbamazepine can suppress FZD8-mediated Wnt/β-catenin signaling. We determined the crystal structure of the complex at 1.7 Å resolution, which reveals that carbamazepine binds at a novel pocket on the FZD8 CRD. The unique residue Tyr52 discriminates FZD8 from the closely related FZD5 and other FZDs for carbamazepine binding. The first small molecule-bound FZD structure provides a basis for anti-FZD drug development. Furthermore, the observed carbamazepine-mediated Wnt signaling inhibition may help to explain the phenomenon of bone loss and increased adipogenesis in some patients during long-term carbamazepine treatment.
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Affiliation(s)
- Yuguang Zhao
- Division of Structural
Biology,
Wellcome Centre for Human Genetics, University
of Oxford, Oxford OX3 7BN, United Kingdom
| | - Jingshan Ren
- Division of Structural
Biology,
Wellcome Centre for Human Genetics, University
of Oxford, Oxford OX3 7BN, United Kingdom
| | - James Hillier
- Division of Structural
Biology,
Wellcome Centre for Human Genetics, University
of Oxford, Oxford OX3 7BN, United Kingdom
| | - Weixian Lu
- Division of Structural
Biology,
Wellcome Centre for Human Genetics, University
of Oxford, Oxford OX3 7BN, United Kingdom
| | - E. Yvonne Jones
- Division of Structural
Biology,
Wellcome Centre for Human Genetics, University
of Oxford, Oxford OX3 7BN, United Kingdom
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30
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Mittl PR, Ernst P, Plückthun A. Chaperone-assisted structure elucidation with DARPins. Curr Opin Struct Biol 2020; 60:93-100. [PMID: 31918361 DOI: 10.1016/j.sbi.2019.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/16/2019] [Accepted: 12/05/2019] [Indexed: 12/14/2022]
Abstract
Designed ankyrin repeat proteins (DARPins) are artificial binding proteins that have found many uses in therapy, diagnostics and biochemical research. They substantially extend the scope of antibody-derived binders. Their high affinity and specificity, rigidity, extended paratope, and facile bacterial production make them attractive for structural biology. Complexes with simple DARPins have been crystallized for a long time, but particularly the rigid helix fusion strategy has opened new opportunities. Rigid DARPin fusions expand crystallization space, enable recruitment of targets in a host lattice and reduce the size limit for cryo-EM. Besides applications in structural biology, rigid DARPin fusions also serve as molecular probes in cells to investigate spatial restraints in targets.
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Affiliation(s)
- Peer Re Mittl
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Patrick Ernst
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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