1
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Bryant P, Noé F. Structure prediction of alternative protein conformations. Nat Commun 2024; 15:7328. [PMID: 39187507 PMCID: PMC11347660 DOI: 10.1038/s41467-024-51507-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 08/07/2024] [Indexed: 08/28/2024] Open
Abstract
Proteins are dynamic molecules whose movements result in different conformations with different functions. Neural networks such as AlphaFold2 can predict the structure of single-chain proteins with conformations most likely to exist in the PDB. However, almost all protein structures with multiple conformations represented in the PDB have been used while training these models. Therefore, it is unclear whether alternative protein conformations can be genuinely predicted using these networks, or if they are simply reproduced from memory. Here, we train a structure prediction network, Cfold, on a conformational split of the PDB to generate alternative conformations. Cfold enables efficient exploration of the conformational landscape of monomeric protein structures. Over 50% of experimentally known nonredundant alternative protein conformations evaluated here are predicted with high accuracy (TM-score > 0.8).
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Affiliation(s)
- Patrick Bryant
- Department of Mathematics and Informatics, Freie Universität Berlin, Arnimallee 12, 14195, Berlin, Germany.
- The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 114 18, Stockholm, Sweden.
- Science for Life Laboratory, 172 21, Solna, Sweden.
| | - Frank Noé
- Department of Mathematics and Informatics, Freie Universität Berlin, Arnimallee 12, 14195, Berlin, Germany
- Microsoft Research AI4Science, Karl-Liebknecht Str. 32, 10178, Berlin, Germany
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2
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Alamgir A, Ghosal S, DeLisa MP, Alabi CA. Bioreversible Anionic Cloaking Enables Intracellular Protein Delivery with Ionizable Lipid Nanoparticles. ACS CENTRAL SCIENCE 2024; 10:1179-1190. [PMID: 38947210 PMCID: PMC11212127 DOI: 10.1021/acscentsci.4c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 07/02/2024]
Abstract
Protein-based therapeutics comprise a rapidly growing subset of pharmaceuticals, but enabling their delivery into cells for intracellular applications has been a longstanding challenge. To overcome the delivery barrier, we explored a reversible, bioconjugation-based approach to modify the surface charge of protein cargos with an anionic "cloak" to facilitate electrostatic complexation and delivery with lipid nanoparticle (LNP) formulations. We demonstrate that the conjugation of lysine-reactive sulfonated compounds can allow for the delivery of various protein cargos using FDA-approved LNP formulations of the ionizable cationic lipid DLin-MC3-DMA (MC3). We apply this strategy to functionally deliver RNase A for cancer cell killing as well as a full-length antibody to inhibit oncogenic β-catenin signaling. Further, we show that LNPs encapsulating cloaked fluorescent proteins distribute to major organs in mice following systemic administration. Overall, our results point toward a generalizable platform that can be employed for intracellular delivery of a wide range of protein cargos.
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Affiliation(s)
- Azmain Alamgir
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Souvik Ghosal
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Matthew P. DeLisa
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
- Cornell
Institute of Biotechnology, Cornell University, Ithaca, New York 14853, United States
| | - Christopher A. Alabi
- Robert
F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
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3
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Ren P, Tiede C, Fanning SW, Adams T, Speirs V, Nelson ER, Cheng C, Moore TW, Greene GL, Tomlinson D, Selvin PR. Labeling of a mutant estrogen receptor with an Affimer in a breast cancer cell line. Biophys J 2022; 121:3651-3662. [PMID: 35778844 PMCID: PMC9617163 DOI: 10.1016/j.bpj.2022.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 05/23/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022] Open
Abstract
Mutations of the intracellular estrogen receptor alpha (ERα) is implicated in 70% of breast cancers. Therefore, it is of considerable interest to image various mutants (L536S, Y537S, D538G) in living cancer cell lines, particularly as a function of various anticancer drugs. We therefore developed a small (13 kDa) Affimer, which, after fluorescent labeling, is able to efficiently label ERα by traveling through temporary pores in the cell membrane, created by the toxin streptolysin O. The Affimer, selected by a phage display, predominantly labels the Y537S mutant and can tell the difference between L536S and D538G mutants. The vast majority of Affimer-ERαY537S is in the nucleus and is capable of an efficient, unrestricted navigation to its target DNA sequence, as visualized by single-molecule fluorescence. The Affimer can also differentiate the effect of selective estrogen receptor modulators. More generally, this is an example of a small binding reagent-an Affimer protein-that can be inserted into living cells with minimal perturbation and high efficiency, to image an endogenous protein.
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Affiliation(s)
- Pin Ren
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Christian Tiede
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Sean W Fanning
- Department of Cancer Research, Loyola University Chicago, Maywood, Illinois
| | - Thomas Adams
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Valerie Speirs
- Institute of Medical Sciences, School of Medicine Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Erik R Nelson
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, Illinois; Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois; Carl R. Woese Institute for Genomic Biology, Anticancer Discovery from Pets to People Theme, University of Illinois Urbana-Champaign, Urbana, Illinois; University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois
| | - Changfeng Cheng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, Illinois
| | - Terry W Moore
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, Illinois; UI Cancer Center, University of Illinois at Chicago (UIC), Chicago, Illinois
| | - Geoffrey L Greene
- Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois
| | - Darren Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Paul R Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois; Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois.
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4
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Zhang Y, Ding X, Xie F, Gao M, Qiu J, Wang Z, Qing L, Yan J, Peng N, Li Y, Xu J, Cai Q, Jin Y, Jiao Y, Liu Y, He H, Zhang S. Targeted Recruitment and Degradation of Estrogen Receptor α by Photothermal Polydopamine Nanoparticles for Breast Tumor Ablation. Adv Healthc Mater 2022; 11:e2200960. [PMID: 35833876 DOI: 10.1002/adhm.202200960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/26/2022] [Indexed: 01/27/2023]
Abstract
The major challenges of photothermal therapy (PTT) toward clinical application are the severe skin injury and inflammation response associated with high power laser irradiation. Herein, polydopamine nanoparticles (PDA-EST and PDA-RAL) targeted to estrogen receptor α (ERα) for efficient ablation of breast tumor under a low irradiation density of 0.1 W cm-2 are reported. These nanoparticles are capable of recruiting ERα on their surface and induce a complete ERα degradation via localized heat. Owing to the ERα targetability, PDA-EST and PDA-RAL strongly suppress the proliferation of breast cancer cells without causing significant inflammation. This work provides a generalized method for enhancing PTT efficacy under low irradiation density.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, 430081, P. R. China
| | - Xin Ding
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, 430081, P. R. China
| | - Fei Xie
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, 430081, P. R. China
| | - Mingjie Gao
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, 430081, P. R. China
| | - Julu Qiu
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, 430081, P. R. China
| | - Ziwei Wang
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, 430081, P. R. China
| | - Luolong Qing
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, 430081, P. R. China
| | - Jiaqi Yan
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, 430081, P. R. China
| | - Na Peng
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, 430081, P. R. China
| | - Yuanyuan Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, P. R. China
| | - Juan Xu
- Hubei Key Laboratory of Mine Environmental Pollution Control & Remediation, College of Chemistry and Chemical Engineering, Hubei Polytechnic University, Huangshi, 435003, P. R. China
| | - Qi Cai
- The first clinical medical college, Anhui Medical University, Hefei, 230032, P. R. China
| | - YuHua Jin
- Hubei Key Laboratory of Mine Environmental Pollution Control & Remediation, College of Chemistry and Chemical Engineering, Hubei Polytechnic University, Huangshi, 435003, P. R. China
| | - Yuanhong Jiao
- Hubei Key Laboratory of Mine Environmental Pollution Control & Remediation, College of Chemistry and Chemical Engineering, Hubei Polytechnic University, Huangshi, 435003, P. R. China
| | - Yi Liu
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, 430081, P. R. China.,State Key Laboratory of Membrane Separation and Membrane Process & Tianjin Key Laboratory of Green Chemical Technology and Process Engineering, School of Chemistry, Tiangong University, Tianjin, 300387, P. R. China
| | - Huan He
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, 430081, P. R. China
| | - Silong Zhang
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, 430081, P. R. China
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5
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Bean ML, Alkohaif RA, Anbari A, Fedraw CP, Ghantasala V, Gojcaj F, Hanein P, Harris MR, Kim D, Proffett DLD, Husseini MH, James EA, O'Rourke BM, Sareini LH, Livezey MR. Computational approaches to identify a novel binding site of BHPI on estrogen receptor alpha. Steroids 2022; 186:109075. [PMID: 35792153 DOI: 10.1016/j.steroids.2022.109075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 06/15/2022] [Accepted: 06/29/2022] [Indexed: 11/26/2022]
Abstract
3,3-bis(4-hydroxyphenyl)-7-methyl-1,3,dihydro-2H-indol-2-one (BHPI) is a biomodulator of Estrogen Receptor alpha (ERα) that targets ERα positive cancer cells by activating the unfolded protein response (UPR). BHPI induces strong and sustained activation of this pathway, eventually resulting in necrotic cell death. While much is known about how BHPI triggers the UPR leading to necrotic cell death, it is not known how BHPI binds to its putative molecular target, ERα. In an effort to identify the binding site of BHPI on ERα, molecular docking studies in AutoDock Vina were utilized. Unexpectedly, BHPI was found to dock more frequently and with significantly better binding affinity to a newly described surface pocket on the ERα ligand-binding domain, compared to the ligand-binding pocket. This work uncovers a novel binding site for small molecules on ERα that is not targeted by classical ligands, such as estrogen and tamoxifen, and may allow for the design of additional anti-cancer drugs that work in distinct ways.
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Affiliation(s)
- Monica L Bean
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US; Meharry Medical College. 1005 Dr DB Todd Jr Blvd, Nashville, TN 37208, US
| | - Reham A Alkohaif
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US
| | - Ahed Anbari
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US
| | - Caela P Fedraw
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US
| | - Vishnu Ghantasala
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US
| | - Florina Gojcaj
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US
| | - Philopateer Hanein
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US
| | - Myles R Harris
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US
| | - Dennis Kim
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US
| | | | - Mahdi H Husseini
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US
| | - Elizabeth A James
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US; Xavier University of Louisiana. 1 Drexel Dr, New Orleans, LA 70125, US
| | - Brendan M O'Rourke
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US
| | - Laila H Sareini
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US
| | - Mara R Livezey
- University of Detroit Mercy. 4001 W. McNichols Rd, Detroit, MI 48221, US.
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6
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Akkapeddi P, Teng KW, Koide S. Monobodies as tool biologics for accelerating target validation and druggable site discovery. RSC Med Chem 2021; 12:1839-1853. [PMID: 34820623 PMCID: PMC8597423 DOI: 10.1039/d1md00188d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022] Open
Abstract
Despite increased investment and technological advancement, new drug approvals have not proportionally increased. Low drug approval rates, particularly for new targets, are linked to insufficient target validation at early stages. Thus, there remains a strong need for effective target validation techniques. Here, we review the use of synthetic binding proteins as tools for drug target validation, with focus on the monobody platform among several advanced synthetic binding protein platforms. Monobodies with high affinity and high selectivity can be rapidly developed against challenging targets, such as KRAS mutants, using protein engineering technologies. They have strong tendency to bind to functional sites and thus serve as drug-like molecules, and they can serve as targeting ligands for constructing bio-PROTACs. Genetically encoded monobodies are effective "tool biologics" for validating intracellular targets. They promote crystallization and help reveal the atomic structures of the monobody-target interface, which can inform drug design. Using case studies, we illustrate the potential of the monobody technology in accelerating target validation and small-molecule drug discovery.
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Affiliation(s)
- Padma Akkapeddi
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine New York NY USA
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7
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Ahmadi MKB, Mohammadi SA, Makvandi M, Mamouei M, Rahmati M, Dehghani H, Wood DW. Recent Advances in the Scaffold Engineering of Protein Binders. Curr Pharm Biotechnol 2021; 22:878-891. [PMID: 32838715 DOI: 10.2174/1389201021999200824101035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 11/22/2022]
Abstract
In recent years, extensive attention has been given to the generation of new classes of ligand- specific binding proteins to supplement monoclonal antibodies. A combination of protein engineering and display technologies has been used to manipulate non-human antibodies for humanization and stabilization purposes or even the generation of new binding proteins. Engineered protein scaffolds can now be directed against therapeutic targets to treat cancer and immunological disorders. Although very few of these scaffolds have successfully passed clinical trials, their remarkable properties such as robust folding, high solubility, and small size motivate their employment as a tool for biology and applied science studies. Here, we have focused on the generation of new non-Ig binding proteins and single domain antibody manipulation, with a glimpse of their applications.
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Affiliation(s)
- Mohammad K B Ahmadi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed A Mohammadi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Manoochehr Makvandi
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Morteza Mamouei
- Department of Animal Science, Ramin Agricultural and Natural Resources University, Ahvaz, Iran
| | - Mohammad Rahmati
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hesam Dehghani
- Stem Cells Regenerative Research Group, Ressearch Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - David W Wood
- Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 W. Woodruff Ave., Columbus, OH 43210, United States
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8
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Xi Z, Liu X, Lin R, Persons JD, Ilina TV, Li W, Dimitrov DS, Ishima R. The reduced form of the antibody CH2 domain. Protein Sci 2021; 30:1895-1903. [PMID: 34107549 DOI: 10.1002/pro.4142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022]
Abstract
Among the immunoglobulin domains, the CH2 domain has the lowest thermal stability, which also depends on amino acid sequence and buffer conditions. To further identify factors that influence CH2 folding and stability, we characterized the domain in the reduced form using differential scanning fluorimetry and nuclear magnetic resonance. We show that the CH2 domain can fold, similarly to the disulfide-bridged form, without forming a disulfide-bridge, even though the protein contains two Cys residues. Although the reduced form exhibits thermal stability more than 15°C lower than the disulfide-bridged form, it does not undergo immediate full oxidization. To explain this phenomenon, we compared CH2 oxidization at different conditions and demonstrate a need for significant fluctuation of the folded conformation to enhance CH2 disulfide-bridge formation. We conclude that, since CH2 can be purified as a folded, semi-stable, reduced protein that can coexist with the oxidized form, verification of the level of oxidization at each step is critical in CH2 engineering studies.
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Affiliation(s)
- Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Xianglei Liu
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rui Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Gastroenterology and Hepatology, Tianjin Medical University, General Hospital, Tianjin, China
| | - John D Persons
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Wei Li
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dimiter S Dimitrov
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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9
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PEG Linker Improves Antitumor Efficacy and Safety of Affibody-Based Drug Conjugates. Int J Mol Sci 2021; 22:ijms22041540. [PMID: 33546481 PMCID: PMC7913616 DOI: 10.3390/ijms22041540] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/13/2022] Open
Abstract
Antibody drug conjugates (ADCs) have become an important modality of clinical cancer treatment. However, traditional ADCs have some limitations, such as reduced permeability in solid tumors due to the high molecular weight of monoclonal antibodies, difficulty in preparation and heterogeneity of products due to the high drug/antibody ratio (4-8 small molecules per antibody). Miniaturized ADCs may be a potential solution, although their short circulation half-life may lead to new problems. In this study, we propose a novel design strategy for miniaturized ADCs in which drug molecules and small ligand proteins are site-specifically coupled via a bifunctional poly(ethylene glycol) (PEG) chain. The results showed that the inserted PEG chains significantly prolonged the circulation half-life but also obviously reduced the cytotoxicity of the conjugates. Compared with the conjugate ZHER2-SMCC-MMAE (HM), which has no PEG insertion, ZHER2-PEG4K-MMAE (HP4KM) and ZHER2-PEG10K-MMAE (HP10KM) with 4 or 10 kDa PEG insertions have 2.5- and 11.2-fold half-life extensions and 4.5- and 22-fold in vitro cytotoxicity reductions, respectively. The combined effect leads to HP10KM having the most ideal tumor therapeutic ability at the same dosages in the animal model, and its off-target toxicity was also reduced by more than 4 times compared with that of HM. These results may indicate that prolonging the half-life is very helpful in improving the therapeutic capacity of miniaturized ADCs. In the future, the design of better strategies that can prolong half-life without affecting cytotoxicity may be useful for further improving the therapeutic potential of these molecules.
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10
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Abstract
The concept of engineering robust protein scaffolds for novel binding functions emerged 20 years ago, one decade after the advent of recombinant antibody technology. Early examples were the Affibody, Monobody (Adnectin), and Anticalin proteins, which were derived from fragments of streptococcal protein A, from the tenth type III domain of human fibronectin, and from natural lipocalin proteins, respectively. Since then, this concept has expanded considerably, including many other protein templates. In fact, engineered protein scaffolds with useful binding specificities, mostly directed against targets of biomedical relevance, constitute an area of active research today, which has yielded versatile reagents as laboratory tools. However, despite strong interest from basic science, only a handful of those protein scaffolds have undergone biopharmaceutical development up to the clinical stage. This includes the abovementioned pioneering examples as well as designed ankyrin repeat proteins (DARPins). Here we review the current state and clinical validation of these next-generation therapeutics.
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Affiliation(s)
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany;
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11
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Chandler PG, Buckle AM. Development and Differentiation in Monobodies Based on the Fibronectin Type 3 Domain. Cells 2020; 9:E610. [PMID: 32143310 PMCID: PMC7140400 DOI: 10.3390/cells9030610] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/24/2020] [Accepted: 03/01/2020] [Indexed: 12/13/2022] Open
Abstract
As a non-antibody scaffold, monobodies based on the fibronectin type III (FN3) domain overcome antibody size and complexity while maintaining analogous binding loops. However, antibodies and their derivatives remain the gold standard for the design of new therapeutics. In response, clinical-stage therapeutic proteins based on the FN3 domain are beginning to use native fibronectin function as a point of differentiation. The small and simple structure of monomeric monobodies confers increased tissue distribution and reduced half-life, whilst the absence of disulphide bonds improves stability in cytosolic environments. Where multi-specificity is challenging with an antibody format that is prone to mis-pairing between chains, multiple FN3 domains in the fibronectin assembly already interact with a large number of molecules. As such, multiple monobodies engineered for interaction with therapeutic targets are being combined in a similar beads-on-a-string assembly which improves both efficacy and pharmacokinetics. Furthermore, full length fibronectin is able to fold into multiple conformations as part of its natural function and a greater understanding of how mechanical forces allow for the transition between states will lead to advanced applications that truly differentiate the FN3 domain as a therapeutic scaffold.
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Affiliation(s)
- Peter G. Chandler
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Australia;
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12
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Deng W, Bates JA, Wei H, Bartoschek MD, Conradt B, Leonhardt H. Tunable light and drug induced depletion of target proteins. Nat Commun 2020; 11:304. [PMID: 31949141 PMCID: PMC6965615 DOI: 10.1038/s41467-019-14160-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 12/12/2019] [Indexed: 12/28/2022] Open
Abstract
Biological processes in development and disease are controlled by the abundance, localization and modification of cellular proteins. We have developed versatile tools based on recombinant E3 ubiquitin ligases that are controlled by light or drug induced heterodimerization for nanobody or DARPin targeted depletion of endogenous proteins in cells and organisms. We use this rapid, tunable and reversible protein depletion for functional studies of essential proteins like PCNA in DNA repair and to investigate the role of CED-3 in apoptosis during Caenorhabditis elegans development. These independent tools can be combined for spatial and temporal depletion of different sets of proteins, can help to distinguish immediate cellular responses from long-term adaptation effects and can facilitate the exploration of complex networks.
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Affiliation(s)
- Wen Deng
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jack A Bates
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hai Wei
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael D Bartoschek
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Barbara Conradt
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany.
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13
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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: 19] [Impact Index Per Article: 4.8] [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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14
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Lopez‐Barbosa N, Ludwicki MB, DeLisa MP. Proteome editing using engineered proteins that hijack cellular quality control machinery. AIChE J 2019. [DOI: 10.1002/aic.16854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Natalia Lopez‐Barbosa
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
| | - Morgan B. Ludwicki
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
| | - Matthew P. DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
- Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University Ithaca New York
- Biochemistry, Molecular and Cell Biology Cornell University Ithaca New York
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15
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Yang XM, Wu ZM, Huang H, Chu XY, Lou J, Xu LX, Chen YT, Wang LQ, Huang OP. Estrogen receptor 1 mutations in 260 cervical cancer samples from Chinese patients. Oncol Lett 2019; 18:2771-2776. [PMID: 31452755 PMCID: PMC6676661 DOI: 10.3892/ol.2019.10612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/04/2019] [Indexed: 01/10/2023] Open
Abstract
Cervical cancer is one of the leading causes of cancer-associated mortality among females; however, the underlying molecular mechanisms of its carcinogenesis remain largely unclear. Previous comprehensive genomic studies have revealed prevalent estrogen receptor 1 (ESR1) mutations in breast cancer, which are rare in certain other types of cancer. To the best of our knowledge, it is unknown whether ESR1 mutations also exist in cervical cancer. Considering the evidence that cervical cancer shares certain genetic aberrations with breast cancer, and that the progression of both breast and cervical cancers can be affected by estrogen, it is possible that cervical cancer may also harbor ESR1 mutations. In the present study, a total of 260 Chinese cervical cancer samples with distinct subtypes were tested for the presence of ESR1 mutations. A total of three heterozygous missense ESR1 mutations, p.K303R (c.908A>G), p.T311M (c.932C>T) and p.Y537C (c.1610A>G), were identified in 3/207 (1.4%) cervical squamous cell carcinoma samples, which were absent in 27 adenosquamous carcinomas and 26 adenocarcinomas samples. Of the three individuals with an ESR1mutation, 1 patient was also diagnosed with ovarian endometriosis and the other 2 patients were diagnosed with a uterine fibroid. A bioinformatics analysis suggested that these ESR1 mutations may be pathogenic by promoting the development of cervical cancer. Furthermore, a previous comprehensive study confirmed that individuals with cervical squamous cell carcinoma possessed ESR1 mutations. These combined studies indicate that ESR1 mutations may participate in the carcinogenesis of cervical squamous cell carcinoma, albeit at a low frequency. In conclusion, the present study identified three potentially pathogenic ESR1 mutations in Chinese cervical squamous cell carcinoma samples, but not in other subtypes.
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Affiliation(s)
- Xin-Min Yang
- College of Medicine, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Zhi-Min Wu
- Department of Management Engineering, Shangrao Vocational and Technical College, Shangrao, Jiangxi 334109, P.R. China
| | - Huang Huang
- Department of Cardiac Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Xiao-Yan Chu
- Department of Gynecological Oncology, Jiangxi Provincial Cancer Hospital, Nanchang, Jiangxi 330029, P.R. China
| | - Jun Lou
- Department of Gynecological Oncology, Jiangxi Provincial Cancer Hospital, Nanchang, Jiangxi 330029, P.R. China
| | - Li-Xian Xu
- College of Medicine, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Yuan-Ting Chen
- College of Medicine, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Li-Qun Wang
- College of Medicine, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Ou-Ping Huang
- College of Medicine, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
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16
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Lappano R, Mallet C, Rizzuti B, Grande F, Galli GR, Byrne C, Broutin I, Boudieu L, Eschalier A, Jacquot Y, Maggiolini M. The Peptide ERα17p Is a GPER Inverse Agonist that Exerts Antiproliferative Effects in Breast Cancer Cells. Cells 2019; 8:cells8060590. [PMID: 31207943 PMCID: PMC6627388 DOI: 10.3390/cells8060590] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/13/2019] [Indexed: 12/18/2022] Open
Abstract
The inhibition of the G protein-coupled estrogen receptor (GPER) offers promising perspectives for the treatment of breast tumors. A peptide corresponding to part of the hinge region/AF2 domain of the human estrogen receptor α (ERα17p, residues 295–311) exerts anti-proliferative effects in various breast cancer cells including those used as triple negative breast cancer (TNBC) models. As preliminary investigations have evoked a role for the GPER in the mechanism of action of this peptide, we focused our studies on this protein using SkBr3 breast cancer cells, which are ideal for GPER evaluation. ERα17p inhibits cell growth by targeting membrane signaling. Identified as a GPER inverse agonist, it co-localizes with GPER and induces the proteasome-dependent downregulation of GPER. It also decreases the level of pEGFR (phosphorylation of epidermal growth factor receptor), pERK1/2 (phosphorylation of extracellular signal-regulated kinase), and c-fos. ERα17p is rapidly distributed in mice after intra-peritoneal injection and is found primarily in the mammary glands. The N-terminal PLMI motif, which presents analogies with the GPER antagonist PBX1, reproduces the effect of the whole ERα17p. Thus, this motif seems to direct the action of the entire peptide, as highlighted by docking and molecular dynamics studies. Consequently, the tetrapeptide PLMI, which can be claimed as the first peptidic GPER disruptor, could open new avenues for specific GPER modulators.
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Affiliation(s)
- Rosamaria Lappano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy.
| | - Christophe Mallet
- NEURO-DOL Basics & Clinical Pharmacology of Pain, INSERM, CHU, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.
- ANALGESIA Institute, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy.
| | - Fedora Grande
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy.
| | - Giulia Raffaella Galli
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy.
| | - Cillian Byrne
- Laboratoire des Biomolécules (LBM), CNRS-UMR 7203, Sorbonne University, Ecole Normale Supérieure, 75252 Paris Cedex 05, France.
| | - Isabelle Broutin
- Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), CNRS-UMR 8038, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 75270 Paris Cedex 06, France.
| | - Ludivine Boudieu
- NEURO-DOL Basics & Clinical Pharmacology of Pain, INSERM, CHU, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.
- ANALGESIA Institute, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.
| | - Alain Eschalier
- NEURO-DOL Basics & Clinical Pharmacology of Pain, INSERM, CHU, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.
- ANALGESIA Institute, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France.
| | - Yves Jacquot
- Laboratoire des Biomolécules (LBM), CNRS-UMR 7203, Sorbonne University, Ecole Normale Supérieure, 75252 Paris Cedex 05, France.
| | - Marcello Maggiolini
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy.
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17
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Toxin Neutralization Using Alternative Binding Proteins. Toxins (Basel) 2019; 11:toxins11010053. [PMID: 30658491 PMCID: PMC6356946 DOI: 10.3390/toxins11010053] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/07/2019] [Accepted: 01/12/2019] [Indexed: 12/20/2022] Open
Abstract
Animal toxins present a major threat to human health worldwide, predominantly through snakebite envenomings, which are responsible for over 100,000 deaths each year. To date, the only available treatment against snakebite envenoming is plasma-derived antivenom. However, despite being key to limiting morbidity and mortality among snakebite victims, current antivenoms suffer from several drawbacks, such as immunogenicity and high cost of production. Consequently, avenues for improving envenoming therapy, such as the discovery of toxin-sequestering monoclonal antibodies against medically important target toxins through phage display selection, are being explored. However, alternative binding protein scaffolds that exhibit certain advantages compared to the well-known immunoglobulin G scaffold, including high stability under harsh conditions and low cost of production, may pose as possible low-cost alternatives to antibody-based therapeutics. There is now a plethora of alternative binding protein scaffolds, ranging from antibody derivatives (e.g., nanobodies), through rationally designed derivatives of other human proteins (e.g., DARPins), to derivatives of non-human proteins (e.g., affibodies), all exhibiting different biochemical and pharmacokinetic profiles. Undeniably, the high level of engineerability and potentially low cost of production, associated with many alternative protein scaffolds, present an exciting possibility for the future of snakebite therapeutics and merit thorough investigation. In this review, a comprehensive overview of the different types of binding protein scaffolds is provided together with a discussion on their relevance as potential modalities for use as next-generation antivenoms.
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18
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Baltz MR, Stephens EA, DeLisa MP. Design and Functional Characterization of Synthetic E3 Ubiquitin Ligases for Targeted Protein Depletion. ACTA ACUST UNITED AC 2019; 10:72-90. [PMID: 30040244 DOI: 10.1002/cpch.37] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A number of techniques now exist for decreasing the expression of cellular proteins without the need for genomic modification. One such technique involves engineered protein chimeras that combine the ubiquitination activity of E3 ubiquitin ligases with the binding affinity and substrate specificity of designer binding proteins (DBPs). These chimeras, called "ubiquibodies," are capable of selectively and controllably steering virtually any protein to the ubiquitin proteasome pathway (UPP) for degradation, making ubiquibodies a powerful addition to the protein knockout toolbox. A distinguishing feature of ubiquibodies is their modularity-simply swapping DBPs can generate a new ubiquibody with specificity for a different substrate protein. Moreover, by employing DBPs that recognize particular protein states (e.g., active versus inactive conformation, mutant versus wild-type, post-translational modification), it becomes possible to deplete certain protein subpopulations while sparing others. This protocol outlines the steps necessary to design and functionally evaluate ubiquibodies for customizable silencing of cellular proteins. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Morgan R Baltz
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York
| | - Erin A Stephens
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York.,Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York
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19
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Affiliation(s)
- Ariel L. Furst
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Matthew B. Francis
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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20
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Richards DA. Exploring alternative antibody scaffolds: Antibody fragments and antibody mimics for targeted drug delivery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 30:35-46. [PMID: 30553519 DOI: 10.1016/j.ddtec.2018.10.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 05/20/2023]
Abstract
The field of targeted therapeutics has benefitted immeasurably from the development of high-affinity antibodies. These important ligands have facilitated the development of effective therapies, particularly when conjugated to potent cytotoxic payloads i.e. in antibody-drug conjugates (ADCs). The success of ADCs is evidenced by rapid adoption within the pharmaceuticals community; many major companies have dedicated ADC research programmes. However, despite the advantages, the field of ADCs has failed to live up to its full potential. Studies have emerged suggesting that traditional IgG scaffolds may not be the optimal format for targeted payload delivery. In response, the protein engineering community has begun to explore alternative high-binding protein scaffolds as antibody mimics. In this short review I will summarise the generation, modification, and application of emerging antibody fragments and synthetic antibody mimics, with a focus on their use as drug carriers. The review aims to highlight the advantages of antibody mimics, and how they could be employed to overcome the issues and limitations of traditional ADCs.
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Affiliation(s)
- Daniel A Richards
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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21
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Senthilkumar T, Zhou L, Gu Q, Liu L, Lv F, Wang S. Conjugated Polymer Nanoparticles with Appended Photo-Responsive Units for Controlled Drug Delivery, Release, and Imaging. Angew Chem Int Ed Engl 2018; 57:13114-13119. [PMID: 30110129 DOI: 10.1002/anie.201807158] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/29/2018] [Indexed: 01/15/2023]
Abstract
Carriers that can afford tunable physical and structural changes are envisioned to address critical issues in controlled drug delivery applications. Herein, photo-responsive conjugated polymer nanoparticles (CPNs) functionalized with donor-acceptor Stenhouse adduct (DASA) and folic acid units for controlled drug delivery and imaging are reported. Upon visible-light (λ=550 nm) irradiation, CPNs simultaneously undergo structure, color, and polarity changes that release encapsulated drugs into the cells. The backbone of CPNs favors FRET to DASA units boosting their fluorescence. Notably, drug-loaded CPNs exhibit excellent biocompatibility in the dark, indicating perfect control of the light trigger over drug release. Delivery of both hydrophilic and hydrophobic drugs with good loading efficiency was demonstrated. This strategy enables remotely controlled drug delivery with visible-light irradiation, which sets an example for designing delivery vehicles for non-invasive therapeutics.
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Affiliation(s)
- Thangaraj Senthilkumar
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lingyun Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,College of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qi Gu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Libing Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,College of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,College of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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22
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Senthilkumar T, Zhou L, Gu Q, Liu L, Lv F, Wang S. Conjugated Polymer Nanoparticles with Appended Photo‐Responsive Units for Controlled Drug Delivery, Release, and Imaging. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Thangaraj Senthilkumar
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Organic SolidsInstitute of ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
| | - Lingyun Zhou
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Organic SolidsInstitute of ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
- College of ChemistryUniversity of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Qi Gu
- State Key Laboratory of Membrane Biology, Institute of ZoologyChinese Academy of Sciences Beijing 100101 P. R. China
| | - Libing Liu
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Organic SolidsInstitute of ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
- College of ChemistryUniversity of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Fengting Lv
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Organic SolidsInstitute of ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
| | - Shu Wang
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Organic SolidsInstitute of ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
- College of ChemistryUniversity of Chinese Academy of Sciences Beijing 100049 P. R. China
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23
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Lau SY, Siau JW, Sobota RM, Wang CI, Zhong P, Lane DP, Ghadessy FJ. Synthetic 10FN3-based mono- and bivalent inhibitors of MDM2/X function. Protein Eng Des Sel 2018; 31:301-312. [PMID: 30169723 PMCID: PMC6277172 DOI: 10.1093/protein/gzy018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/10/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Engineered non-antibody scaffold proteins constitute a rapidly growing technology for diagnostics and modulation/perturbation of protein function. Here, we describe the rapid and systematic development of high-affinity 10FN3 domain inhibitors of the MDM2 and MDMX proteins. These are often overexpressed in cancer and represent attractive drug targets. Using facile in vitro expression and pull-down assay methodology, numerous design iterations addressing insertion site(s) and spacer length were screened for optimal presentation of an MDM2/X dual peptide inhibitor in the 10FN3 scaffold. Lead inhibitors demonstrated robust, on-target cellular inhibition of MDM2/X leading to activation of the p53 tumor suppressor. Significant improvement to target engagement was observed by increasing valency within a single 10FN3 domain, which has not been demonstrated previously. We further established stable reporter cell lines with tunable expression of EGFP-fused 10FN3 domain inhibitors, and showed their intracellular location to be contingent on target engagement. Importantly, competitive inhibition of MDM2/X by small molecules and cell-penetrating peptides led to a readily observable phenotype, indicating significant potential of the developed platform as a robust tool for cell-based drug screening.
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Affiliation(s)
- S -Y Lau
- p53 Laboratory (p53Lab), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, Singapore
| | - J W Siau
- p53 Laboratory (p53Lab), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, Singapore
| | - R M Sobota
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Dr, Singapore, Singapore
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, Singapore
| | - C -I Wang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, Singapore
| | - P Zhong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, Singapore
| | - D P Lane
- p53 Laboratory (p53Lab), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, Singapore
| | - F J Ghadessy
- p53 Laboratory (p53Lab), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, Singapore
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24
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Gorman K, McGinnis J, Kay B. Generating FN3-Based Affinity Reagents Through Phage Display. ACTA ACUST UNITED AC 2018; 10:e39. [PMID: 29927113 DOI: 10.1002/cpch.39] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Antibodies are useful tools for detecting individual proteins in complex samples and for learning about their location, amount, binding partners, and function in cells. Unfortunately, generating antibodies is time consuming and laborious, and their affinity and/or specificity is often limited. This protocol offers a fast and inexpensive alternative to generate antibody surrogates through phage display of a library of fibronectin type III (FN3) monobody variants and affinity selection for binders. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Kevin Gorman
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois
| | - Jennifer McGinnis
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois
| | - Brian Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois
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25
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Furst AL, Smith MJ, Francis MB. New Techniques for the Generation and Analysis of Tailored Microbial Systems on Surfaces. Biochemistry 2018; 57:3017-3026. [DOI: 10.1021/acs.biochem.8b00324] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ariel L. Furst
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Matthew J. Smith
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Matthew B. Francis
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720-1460, United States
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26
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Grande F, Rizzuti B, Occhiuzzi MA, Ioele G, Casacchia T, Gelmini F, Guzzi R, Garofalo A, Statti G. Identification by Molecular Docking ofHomoisoflavones from Leopoldia comosa as Ligands of Estrogen Receptors. Molecules 2018; 23:molecules23040894. [PMID: 29649162 PMCID: PMC6017050 DOI: 10.3390/molecules23040894] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 02/07/2023] Open
Abstract
The physiological responses to estrogen hormones are mediated within specific tissues by at least two distinct receptors, ERα and ERβ. Several natural and synthetic molecules show activity by interacting with these proteins. In particular, a number of vegetal compounds known as phytoestrogens shows estrogenic or anti-estrogenic activity. The majority of these compounds belongs to the isoflavones family and the most representative one, genistein, shows anti-proliferative effects on various hormone-sensitive cancer cells, including breast, ovarian and prostate cancer. In this work we describe the identification of structurally related homoisoflavones isolated from Leopoldia comosa (L.) Parl. (L. comosa), a perennial bulbous plant, potentially useful as hormonal substitutes or complements in cancer treatments. Two of these compounds have been selected as potential ligands of estrogen receptors (ERs) and the interaction with both isoforms of estrogen receptors have been investigated through molecular docking on their crystallographic structures. The results provide evidence of the binding of these compounds to the target receptors and their interactions with key residues of the active sites of the two proteins, and thus they could represent suitable leads for the development of novel tools for the dissection of ER signaling and the development of new pharmacological treatments in hormone-sensitive cancers.
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Affiliation(s)
- Fedora Grande
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Ampl. Polifunzionale, Via P. Bucci, 87036 Rende (CS), Italy.
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, 87036 Rende (CS), Italy.
| | - Maria A Occhiuzzi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Ampl. Polifunzionale, Via P. Bucci, 87036 Rende (CS), Italy.
| | - Giuseppina Ioele
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Ampl. Polifunzionale, Via P. Bucci, 87036 Rende (CS), Italy.
| | - Teresa Casacchia
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Ampl. Polifunzionale, Via P. Bucci, 87036 Rende (CS), Italy.
| | - Fabrizio Gelmini
- Department of Environmental Science and Policy-ESP, University of Milan, Via Celoria 2, 20133 Milan, Italy.
| | - Rita Guzzi
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, 87036 Rende (CS), Italy.
- Department of Physics, University of Calabria, Via P. Bucci, 87036 Rende (CS), Italy.
| | - Antonio Garofalo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Ampl. Polifunzionale, Via P. Bucci, 87036 Rende (CS), Italy.
| | - Giancarlo Statti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Ampl. Polifunzionale, Via P. Bucci, 87036 Rende (CS), Italy.
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Wilson LJ, Linley A, Hammond DE, Hood FE, Coulson JM, MacEwan DJ, Ross SJ, Slupsky JR, Smith PD, Eyers PA, Prior IA. New Perspectives, Opportunities, and Challenges in Exploring the Human Protein Kinome. Cancer Res 2017; 78:15-29. [DOI: 10.1158/0008-5472.can-17-2291] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/22/2017] [Accepted: 10/31/2017] [Indexed: 11/16/2022]
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28
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Sha F, Salzman G, Gupta A, Koide S. Monobodies and other synthetic binding proteins for expanding protein science. Protein Sci 2017; 26:910-924. [PMID: 28249355 PMCID: PMC5405424 DOI: 10.1002/pro.3148] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/20/2023]
Abstract
Synthetic binding proteins are constructed using nonantibody molecular scaffolds. Over the last two decades, in‐depth structural and functional analyses of synthetic binding proteins have improved combinatorial library designs and selection strategies, which have resulted in potent platforms that consistently generate binding proteins to diverse targets with affinity and specificity that rival those of antibodies. Favorable attributes of synthetic binding proteins, such as small size, freedom from disulfide bond formation and ease of making fusion proteins, have enabled their unique applications in protein science, cell biology and beyond. Here, we review recent studies that illustrate how synthetic binding proteins are powerful probes that can directly link structure and function, often leading to new mechanistic insights. We propose that synthetic proteins will become powerful standard tools in diverse areas of protein science, biotechnology and medicine.
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Affiliation(s)
- Fern Sha
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Gabriel Salzman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Ankit Gupta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016.,Department of Biochemistry and Molecular Pharmacology New York University School of Medicine, New York, NY, 10016
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29
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Furst A, Hoepker AC, Francis MB. Quantifying Hormone Disruptors with an Engineered Bacterial Biosensor. ACS CENTRAL SCIENCE 2017; 3:110-116. [PMID: 28280777 PMCID: PMC5324086 DOI: 10.1021/acscentsci.6b00322] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Indexed: 05/30/2023]
Abstract
Endocrine disrupting compounds are found in increasing amounts in our environment, originating from pesticides, plasticizers, and pharmaceuticals, among other sources. Although the full impact of these compounds is still under study, they have already been implicated in diseases such as obesity, diabetes, and cancer. The list of chemicals that disrupt normal hormone function is growing at an alarming rate, making it crucially important to find sources of contamination and identify new compounds that display this ability. However, there is currently no broad-spectrum, rapid test for these compounds, as they are difficult to monitor because of their high potency and chemical dissimilarity. To address this, we have developed a new detection strategy for endocrine disrupting compounds that is both fast and portable, and it requires no specialized skills to perform. This system is based on a native estrogen receptor construct expressed on the surface of Escherichia coli, which enables both the detection of many detrimental compounds and signal amplification from impedance measurements due to the binding of bacteria to a modified electrode. With this approach, sub-ppb levels of estradiol and ppm levels of bisphenol A are detected in complex solutions. Rather than responding to individual components, this system reports the total estrogenic activity of a sample using the most relevant biological receptor. As an applied example, estrogenic chemicals released from a plastic baby bottle following microwave heating were detectable with this technique. This approach should be broadly applicable to the detection of chemically diverse classes of compounds that bind to a single receptor.
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Affiliation(s)
- Ariel
L. Furst
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Alexander C. Hoepker
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Matthew B. Francis
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
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30
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A Conjugate Based on Anti-HER2 Diaffibody and Auristatin E Targets HER2-Positive Cancer Cells. Int J Mol Sci 2017; 18:ijms18020401. [PMID: 28216573 PMCID: PMC5343935 DOI: 10.3390/ijms18020401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/20/2017] [Accepted: 01/31/2017] [Indexed: 01/29/2023] Open
Abstract
Antibody-drug conjugates (ADCs) have recently emerged as efficient and selective cancer treatment therapeutics. Currently, alternative forms of drug carriers that can replace monoclonal antibodies are under intensive investigation. Here, a cytotoxic conjugate of an anti-HER2 (Human Epidermal Growth Factor Receptor 2) diaffibody with monomethyl-auristatin E (MMAE) is proposed as a potential anticancer therapeutic. The anti-HER2 diaffibody was based on the ZHER2:4 affibody amino acid sequence. The anti-HER2 diaffibody has been expressed as a His-tagged protein in E. coli and purified by Ni-nitrilotriacetyl (Ni-NTA) agarose chromatography. The molecule was properly folded, and the high affinity and specificity of its interaction with HER2 was confirmed by surface plasmon resonance (SPR) and flow cytometry, respectively. The (ZHER2:4)2DCS-MMAE conjugate was obtained by coupling the maleimide group linked with MMAE to cysteines, which were introduced in a drug conjugation sequence (DCS). Cytotoxicity of the conjugate was evaluated using the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide MTT assay and the xCELLigence Real-Time Cell Analyzer. Our experiments demonstrated that the conjugate delivered auristatin E specifically to HER2-positive tumor cells, which finally led to their death. These results indicate that the cytotoxic diaffibody conjugate is a highly potent molecule for the treatment of various types of cancer overexpressing HER2 receptors.
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31
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Banerjee A, Ray S. Mutations and interactions in human ERα and bZIP proteins: An in silico approach for cell signaling in breast oncology. Gene 2017; 610:90-102. [PMID: 28111258 DOI: 10.1016/j.gene.2017.01.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/04/2016] [Accepted: 01/17/2017] [Indexed: 01/15/2023]
Abstract
I. BACKGROUND Metastasis of breast cancer serves the most aggravating cause for transience in breast cancer patients. Accumulating evidences suggest that signal transduction in human breast cancers commences in estrogen-reliant pattern via signaling of the estrogen-receptor α-subunit (ERα) and XBP-1 (bZIP-domain) proteins. Furthermore, earlier investigations from SAGE and GST pull-down assay, also state that a point mutation in ERα leads to a risky factor by resulting into hyper-responsiveness towards estrogen and increased proliferation of breast cancer cells. So, a molecular-level exploration into the signaling mechanism is a prime requisite for future clinical and therapeutic progress. II. METHODS AND RESULTS Present study explores primarily the residual participation of the two essential proteins from humans to boost the signaling mechanism in malignant breast tumors. So, 3D structures of the respective monomer proteins were demonstrated and mutated protein was homology modeled after the satisfaction of the stereo-chemical features. The functionality was observed to be conserved after mutation. Abrupt increment in protein-protein interactions was studied for the individual optimized and Molecular Dynamics simulated protein complexes. Revelation from supportive statistical significances for several energy calculations, solvent accessibility areas, electrostatic surface potentials and interaction studies led to confer that after mutation, the complex and the individual protein were the most stable and the best interactive one. For metastasis in breast cancer cells, polar charged residues hold a significant contribution. III. CONCLUSION Therefore, this investigation provides a cogent framework for the interactive studies associated with breast cancer and an exposure towards the lethal impact on mutation.
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Affiliation(s)
- Arundhati Banerjee
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur, West Bengal, India.
| | - Sujay Ray
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, West Bengal, India; Amity Institute of Biotechnology, Amity University, Kolkata, West Bengal, India.
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32
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Cetin M, Evenson WE, Gross GG, Jalali-Yazdi F, Krieger D, Arnold D, Takahashi TT, Roberts RW. RasIns: Genetically Encoded Intrabodies of Activated Ras Proteins. J Mol Biol 2016; 429:562-573. [PMID: 27865780 DOI: 10.1016/j.jmb.2016.11.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 11/11/2016] [Accepted: 11/12/2016] [Indexed: 01/11/2023]
Abstract
K- and H-Ras are the most commonly mutated genes in human tumors and are critical for conferring and maintaining the oncogenic phenotype in tumors with poor prognoses. Here, we design genetically encoded antibody-like ligands (intrabodies) that recognize active, GTP-bound K- and H-Ras. These ligands, which use the 10th domain of human fibronectin as their scaffold, are stable inside the cells and when fused with a fluorescent protein label, the constitutively active G12V mutant H-Ras. Primary selection of ligands against Ras with mRNA display resulted in an intrabody (termed RasIn1) that binds with a KD of 2.1μM to H-Ras(G12V) (GTP), excellent state selectivity, and remarkable specificity for K- and H-Ras. RasIn1 recognizes residues in the Switch I region of Ras, similar to Raf-RBD, and competes with Raf-RBD for binding. An affinity maturation selection based on RasIn1 resulted in RasIn2, which binds with a KD of 120nM and also retains excellent state selectivity. Both of these intrabodies colocalize with H-Ras, K-Ras, and G12V mutants inside the cells, providing new potential tools to monitor and modulate Ras-mediated signaling. Finally, RasIn1 and Rasin2 both display selectivity for the G12V mutants as compared with wild-type Ras providing a potential route for mutant selective recognition of Ras.
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Affiliation(s)
- Mehmet Cetin
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - William E Evenson
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Garrett G Gross
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Farzad Jalali-Yazdi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel Krieger
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Don Arnold
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Terry T Takahashi
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Richard W Roberts
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA.
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33
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Baker AM, Van Noorden S, Rodriguez-Justo M, Cohen P, Wright NA, Lampert IA. Distribution of the c-MYC gene product in colorectal neoplasia. Histopathology 2016; 69:222-9. [PMID: 26826706 PMCID: PMC4949543 DOI: 10.1111/his.12939] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/27/2016] [Indexed: 12/14/2022]
Abstract
AIMS Recent attempts to study MYC distribution in human samples have been confounded by a lack of agreement in immunohistochemical staining between antibodies targeting the N-terminus and those targeting the C-terminus of the MYC protein. The aim of this study was to use a novel in-situ hybridization (ISH) approach to detect MYC mRNA in clinically relevant samples, and thereby determine the reliability of MYC-targeting antibodies. METHODS AND RESULTS We performed immunohistochemistry on human formalin-fixed paraffin embedded normal colon (n = 15), hyperplastic polyp (n = 4) and neoplastic colon samples (n = 55), using the N-terminally directed antibody Y69, and the C-terminally directed antibody 9E10. The MYC protein distributions were then compared with the location of MYC mRNA, determined by ISH. We found that the localization of MYC mRNA correlated well with the protein distribution determined with the N-terminally directed antibody Y69, and was also associated with expression of the proliferation marker Ki67. The protein distribution determined with the C-terminally directed antibody 9E10 was not always associated with MYC mRNA, Y69, or Ki67, and indeed often showed a reciprocal pattern of expression, with staining being strongest in non-proliferating cells. CONCLUSIONS The observed discrepancy between the staining patterns suggests that the significance of 9E10 in immunohistochemical staining is currently uncertain, and therefore should be interpreted with caution.
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Affiliation(s)
- Ann-Marie Baker
- Centre for Tumour Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Susan Van Noorden
- Department of Histopathology, Imperial College London, Hammersmith Hospital, London, UK
| | | | - Patrizia Cohen
- Department of Cellular Pathology, Clarence Memorial Wing, St Mary's Hospital, London, UK
| | - Nicholas A Wright
- Centre for Tumour Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Irvin A Lampert
- Department of Histopathology, West Middlesex University Hospital, Isleworth, UK
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34
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Rosen CB, Kwant RL, MacDonald JI, Rao M, Francis MB. Capture and Recycling of Sortase A through Site-Specific Labeling with Lithocholic Acid. Angew Chem Int Ed Engl 2016; 55:8585-9. [PMID: 27239057 DOI: 10.1002/anie.201602353] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/26/2016] [Indexed: 11/05/2022]
Abstract
Enzyme-mediated protein modification often requires large amounts of biocatalyst, adding significant costs to the process and limiting industrial applications. Herein, we demonstrate a scalable and straightforward strategy for the efficient capture and recycling of enzymes using a small-molecule affinity tag. A proline variant of an evolved sortase A (SrtA 7M) was N-terminally labeled with lithocholic acid (LA)-an inexpensive bile acid that exhibits strong binding to β-cyclodextrin (βCD). Capture and recycling of the LA-Pro-SrtA 7M conjugate was achieved using βCD-modified sepharose resin. The LA-Pro-SrtA 7M conjugate retained full enzymatic activity, even after multiple rounds of recycling.
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Affiliation(s)
- Christian B Rosen
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720-1460, USA.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Richard L Kwant
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720-1460, USA.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - James I MacDonald
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720-1460, USA.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Meera Rao
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720-1460, USA.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720-1460, USA. .,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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35
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Rosen CB, Kwant RL, MacDonald JI, Rao M, Francis MB. Capture and Recycling of Sortase A through Site‐Specific Labeling with Lithocholic Acid. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602353] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Christian B. Rosen
- Department of Chemistry University of California, Berkeley Berkeley CA 94720-1460 USA
- Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Richard L. Kwant
- Department of Chemistry University of California, Berkeley Berkeley CA 94720-1460 USA
- Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - James I. MacDonald
- Department of Chemistry University of California, Berkeley Berkeley CA 94720-1460 USA
- Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Meera Rao
- Department of Chemistry University of California, Berkeley Berkeley CA 94720-1460 USA
- Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Matthew B. Francis
- Department of Chemistry University of California, Berkeley Berkeley CA 94720-1460 USA
- Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
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36
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Huang R, Fang P, Hao Z, Kay BK. Directed Evolution of a Highly Specific FN3 Monobody to the SH3 Domain of Human Lyn Tyrosine Kinase. PLoS One 2016; 11:e0145872. [PMID: 26731115 PMCID: PMC4701441 DOI: 10.1371/journal.pone.0145872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/09/2015] [Indexed: 11/26/2022] Open
Abstract
Affinity reagents of high affinity and specificity are very useful for studying the subcellular locations and quantities of individual proteins. To generate high-quality affinity reagents for human Lyn tyrosine kinase, a phage display library of fibronectin type III (FN3) monobodies was affinity selected with a recombinant form of the Lyn SH3 domain. While a highly specific monobody, TA8, was initially isolated, we chose to improve its affinity through directed evolution. A secondary library of 1.2 × 109 variants was constructed and screened by affinity selection, yielding three variants, two of which have affinities of ~ 40 nM, a 130-fold increase over the original TA8 monobody. One of the variants, 2H7, displayed high specificity to the Lyn SH3 domain, as shown by ELISA and probing arrays of 150 SH3 domains. Furthermore, the 2H7 monobody was able to pull down endogenous Lyn from a lysate of Burkitt's lymphoma cells, thereby demonstrating its utility as an affinity reagent for detecting Lyn in a complex biological mixture.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (RH); (BK)
| | - Pete Fang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Zengping Hao
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Brian K. Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (RH); (BK)
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37
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Helma J, Cardoso MC, Muyldermans S, Leonhardt H. Nanobodies and recombinant binders in cell biology. J Cell Biol 2015; 209:633-44. [PMID: 26056137 PMCID: PMC4460151 DOI: 10.1083/jcb.201409074] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Antibodies are key reagents to investigate cellular processes. The development of recombinant antibodies and binders derived from natural protein scaffolds has expanded traditional applications, such as immunofluorescence, binding arrays, and immunoprecipitation. In addition, their small size and high stability in ectopic environments have enabled their use in all areas of cell research, including structural biology, advanced microscopy, and intracellular expression. Understanding these novel reagents as genetic modules that can be integrated into cellular pathways opens up a broad experimental spectrum to monitor and manipulate cellular processes.
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Affiliation(s)
- Jonas Helma
- Department of Biology II, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich, 82152 Planegg-Martinsried, Germany
| | - M Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich, 82152 Planegg-Martinsried, Germany
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38
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Specific GFP-binding artificial proteins (αRep): a new tool for in vitro to live cell applications. Biosci Rep 2015; 35:BSR20150080. [PMID: 26182430 PMCID: PMC4613692 DOI: 10.1042/bsr20150080] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/23/2015] [Indexed: 02/08/2023] Open
Abstract
Artificial proteins, named αRep, binding tightly and specifically to EGFP are described. The structures of αRep–EGFP complexes explain how αRep recognize their cognate partner. Specific αRep can be used for biochemical or live cells experiments. A family of artificial proteins, named αRep, based on a natural family of helical repeat was previously designed. αRep members are efficiently expressed, folded and extremely stable proteins. A large αRep library was constructed creating proteins with a randomized interaction surface. In the present study, we show that the αRep library is an efficient source of tailor-made specific proteins with direct applications in biochemistry and cell biology. From this library, we selected by phage display αRep binders with nanomolar dissociation constants against the GFP. The structures of two independent αRep binders in complex with the GFP target were solved by X-ray crystallography revealing two totally different binding modes. The affinity of the selected αReps for GFP proved sufficient for practically useful applications such as pull-down experiments. αReps are disulfide free proteins and are efficiently and functionally expressed in eukaryotic cells: GFP-specific αReps are clearly sequestrated by their cognate target protein addressed to various cell compartments. These results suggest that αRep proteins with tailor-made specificity can be selected and used in living cells to track, modulate or interfere with intracellular processes.
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39
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Khandelwal N, Doke DS, Khandare JJ, Jawale PV, Biradar AV, Giri AP. Bio-physical evaluation and in vivo delivery of plant proteinase inhibitor immobilized on silica nanospheres. Colloids Surf B Biointerfaces 2015; 130:84-92. [DOI: 10.1016/j.colsurfb.2015.03.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 03/05/2015] [Accepted: 03/30/2015] [Indexed: 11/26/2022]
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40
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Iacob RE, Krystek SR, Huang RYC, Wei H, Tao L, Lin Z, Morin PE, Doyle ML, Tymiak AA, Engen JR, Chen G. Hydrogen/deuterium exchange mass spectrometry applied to IL-23 interaction characteristics: potential impact for therapeutics. Expert Rev Proteomics 2015; 12:159-69. [PMID: 25711416 DOI: 10.1586/14789450.2015.1018897] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
IL-23 is an important therapeutic target for the treatment of inflammatory diseases. Adnectins are targeted protein therapeutics that are derived from domain III of human fibronectin and have a similar protein scaffold to antibodies. Adnectin 2 was found to bind to IL-23 and compete with the IL-23/IL-23R interaction, posing a potential protein therapeutic. Hydrogen/deuterium exchange mass spectrometry and computational methods were applied to probe the binding interactions between IL-23 and Adnectin 2 and to determine the correlation between the two orthogonal methods. This review summarizes the current structural knowledge about IL-23 and focuses on the applicability of hydrogen/deuterium exchange mass spectrometry to investigate the higher order structure of proteins, which plays an important role in the discovery of new and improved biotherapeutics.
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Affiliation(s)
- Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
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41
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Characterization of monobody scaffold interactions with ligand via force spectroscopy and steered molecular dynamics. Sci Rep 2015; 5:8247. [PMID: 25650239 PMCID: PMC4316159 DOI: 10.1038/srep08247] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/31/2014] [Indexed: 12/22/2022] Open
Abstract
Monobodies are antibody alternatives derived from fibronectin that are thermodynamically stable, small in size, and can be produced in bacterial systems. Monobodies have been engineered to bind a wide variety of target proteins with high affinity and specificity. Using alanine-scanning mutagenesis simulations, we identified two scaffold residues that are critical to the binding interaction between the monobody YS1 and its ligand, maltose-binding protein (MBP). Steered molecular dynamics (SMD) simulations predicted that the E47A and R33A mutations in the YS1 scaffold substantially destabilize the YS1-MBP interface by reducing the bond rupture force and the lifetime of single hydrogen bonds. SMD simulations further indicated that the R33A mutation weakens the hydrogen binding between all scaffold residues and MBP and not just between R33 and MBP. We validated the simulation data and characterized the effects of mutations on YS1-MBP binding by using single-molecule force spectroscopy and surface plasmon resonance. We propose that interfacial stability resulting from R33 of YS1 stacking with R344 of MBP synergistically stabilizes both its own bond and the interacting scaffold residues of YS1. Our integrated approach improves our understanding of the monobody scaffold interactions with a target, thus providing guidance for the improved engineering of monobodies.
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42
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Iacob RE, Chen G, Ahn J, Houel S, Wei H, Mo J, Tao L, Cohen D, Xie D, Lin Z, Morin PE, Doyle ML, Tymiak AA, Engen JR. The influence of adnectin binding on the extracellular domain of epidermal growth factor receptor. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2093-2102. [PMID: 25223306 PMCID: PMC4224629 DOI: 10.1007/s13361-014-0973-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/29/2014] [Accepted: 08/03/2014] [Indexed: 06/03/2023]
Abstract
The precise and unambiguous elucidation and characterization of interactions between a high affinity recognition entity and its cognate protein provides important insights for the design and development of drugs with optimized properties and efficacy. In oncology, one important target protein has been shown to be the epidermal growth factor receptor (EGFR) through the development of therapeutic anticancer antibodies that are selective inhibitors of EGFR activity. More recently, smaller protein derived from the 10th type III domain of human fibronectin termed an adnectin has also been shown to inhibit EGFR in clinical studies. The mechanism of EGFR inhibition by either an adnectin or an antibody results from specific binding of the high affinity protein to the extracellular portion of EGFR (exEGFR) in a manner that prevents phosphorylation of the intracellular kinase domain of the receptor and thereby blocks intracellular signaling. Here, the structural changes induced upon binding were studied by probing the solution conformations of full length exEGFR alone and bound to a cognate adnectin through hydrogen/deuterium exchange mass spectrometry (HDX MS). The effects of binding in solution were identified and compared with the structure of a bound complex determined by X-ray crystallography.ᅟ
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Affiliation(s)
- Roxana E. Iacob
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA USA
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Joomi Ahn
- Waters Corporation, Milford, MA, USA
| | | | - Hui Wei
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Jingjie Mo
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Li Tao
- Biologics Manufacturing and Process Development, Global Manufacturing and Supply, Bristol-Myers Squibb Company, Hopewell, NJ, USA
| | - Daniel Cohen
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Dianlin Xie
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Zheng Lin
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Paul E. Morin
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Michael L. Doyle
- Protein Science, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Adrienne A. Tymiak
- Bioanalytical and Discovery Analytical Sciences, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - John R. Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA USA
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Yan Y, Chen G, Wei H, Huang RYC, Mo J, Rempel DL, Tymiak AA, Gross ML. Fast photochemical oxidation of proteins (FPOP) maps the epitope of EGFR binding to adnectin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2084-92. [PMID: 25267085 PMCID: PMC4224620 DOI: 10.1007/s13361-014-0993-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/15/2014] [Accepted: 08/21/2014] [Indexed: 05/11/2023]
Abstract
Epitope mapping is an important tool for the development of monoclonal antibodies, mAbs, as therapeutic drugs. Recently, a class of therapeutic mAb alternatives, adnectins, has been developed as targeted biologics. They are derived from the 10th type III domain of human fibronectin ((10)Fn3). A common approach to map the epitope binding of these therapeutic proteins to their binding partners is X-ray crystallography. Although the crystal structure is known for Adnectin 1 binding to human epidermal growth factor receptor (EGFR), we seek to determine complementary binding in solution and to test the efficacy of footprinting for this purpose. As a relatively new tool in structural biology and complementary to X-ray crystallography, protein footprinting coupled with mass spectrometry is promising for protein-protein interaction studies. We report here the use of fast photochemical oxidation of proteins (FPOP) coupled with MS to map the epitope of EGFR-Adnectin 1 at both the peptide and amino-acid residue levels. The data correlate well with the previously determined epitopes from the crystal structure and are consistent with HDX MS data, which are presented in an accompanying paper. The FPOP-determined binding interface involves various amino-acid and peptide regions near the N terminus of EGFR. The outcome adds credibility to oxidative labeling by FPOP for epitope mapping and motivates more applications in the therapeutic protein area as a stand-alone method or in conjunction with X-ray crystallography, NMR, site-directed mutagenesis, and other orthogonal methods.
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Affiliation(s)
- Yuetian Yan
- Center for Biomedical and Bioorganic Mass Spectrometry, Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130-4899, USA
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Dunker AK, Bondos SE, Huang F, Oldfield CJ. Intrinsically disordered proteins and multicellular organisms. Semin Cell Dev Biol 2014; 37:44-55. [PMID: 25307499 DOI: 10.1016/j.semcdb.2014.09.025] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/15/2014] [Accepted: 09/30/2014] [Indexed: 12/12/2022]
Abstract
Intrinsically disordered proteins (IDPs) and IDP regions lack stable tertiary structure yet carry out numerous biological functions, especially those associated with signaling, transcription regulation, DNA condensation, cell division, and cellular differentiation. Both post-translational modifications (PTMs) and alternative splicing (AS) expand the functional repertoire of IDPs. Here we propose that an "IDP-based developmental toolkit," which is comprised of IDP regions, PTMs, especially multiple PTMs, within these IDP regions, and AS events within segments of pre-mRNA that code for these same IDP regions, allows functional diversification and environmental responsiveness for molecules that direct the development of complex metazoans.
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Affiliation(s)
- A Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, United States.
| | - Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, United States.
| | - Fei Huang
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, United States.
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, United States.
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45
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Ng HW, Perkins R, Tong W, Hong H. Versatility or promiscuity: the estrogen receptors, control of ligand selectivity and an update on subtype selective ligands. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2014; 11:8709-42. [PMID: 25162709 PMCID: PMC4198987 DOI: 10.3390/ijerph110908709] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 12/20/2022]
Abstract
The estrogen receptors (ERs) are a group of versatile receptors. They regulate an enormity of processes starting in early life and continuing through sexual reproduction, development, and end of life. This review provides a background and structural perspective for the ERs as part of the nuclear receptor superfamily and discusses the ER versatility and promiscuity. The wide repertoire of ER actions is mediated mostly through ligand-activated transcription factors and many DNA response elements in most tissues and organs. Their versatility, however, comes with the drawback of promiscuous interactions with structurally diverse exogenous chemicals with potential for a wide range of adverse health outcomes. Even when interacting with endogenous hormones, ER actions can have adverse effects in disease progression. Finally, how nature controls ER specificity and how the subtle differences in receptor subtypes are exploited in pharmaceutical design to achieve binding specificity and subtype selectivity for desired biological response are discussed. The intent of this review is to complement the large body of literature with emphasis on most recent developments in selective ER ligands.
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Affiliation(s)
- Hui Wen Ng
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Roger Perkins
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
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Kaiser PD, Maier J, Traenkle B, Emele F, Rothbauer U. Recent progress in generating intracellular functional antibody fragments to target and trace cellular components in living cells. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1933-1942. [PMID: 24792387 DOI: 10.1016/j.bbapap.2014.04.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 04/16/2014] [Accepted: 04/21/2014] [Indexed: 02/04/2023]
Abstract
In biomedical research there is an ongoing demand for new technologies, which help to elucidate disease mechanisms and provide the basis to develop novel therapeutics. In this context a comprehensive understanding of cellular processes and their pathophysiology based on reliable information on abundance, localization, posttranslational modifications and dynamic interactions of cellular components is indispensable. Besides their significant impact as therapeutic molecules, antibodies are arguably the most powerful research tools to study endogenous proteins and other cellular components. However, for cellular diagnostics their use is restricted to endpoint assays using fixed and permeabilized cells. Alternatively, live cell imaging using fluorescent protein-tagged reporters is widely used to study protein localization and dynamics in living cells. However, only artificially introduced chimeric proteins are visualized, whereas the endogenous proteins, their posttranslational modifications as well as non-protein components of the cell remain invisible and cannot be analyzed. To overcome these limitations, traceable intracellular binding molecules provide new opportunities to perform cellular diagnostics in real time. In this review we summarize recent progress in the generation of intracellular and cell penetrating antibodies and their application to target and trace cellular components in living cells. We highlight recent advances in the structural formulation of recombinant antibody formats, reliable screening protocols and sophisticated cellular targeting technologies and propose that such intrabodies will become versatile research tools for real time cell-based diagnostics including target validation and live cell imaging. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.
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Affiliation(s)
- Philipp D Kaiser
- Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany; Department of Pharmaceutical Biotechnology, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Julia Maier
- Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany; Department of Pharmaceutical Biotechnology, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Bjoern Traenkle
- Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany; Department of Pharmaceutical Biotechnology, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Felix Emele
- Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany; Department of Pharmaceutical Biotechnology, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany; Department of Pharmaceutical Biotechnology, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany.
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Portnoff AD, Stephens EA, Varner JD, DeLisa MP. Ubiquibodies, synthetic E3 ubiquitin ligases endowed with unnatural substrate specificity for targeted protein silencing. J Biol Chem 2014; 289:7844-55. [PMID: 24474696 DOI: 10.1074/jbc.m113.544825] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The ubiquitin-proteasome pathway (UPP) is the main route of protein degradation in eukaryotic cells and is a common mechanism through which numerous cellular pathways are regulated. To date, several reverse genetics techniques have been reported that harness the power of the UPP for selectively reducing the levels of otherwise stable proteins. However, each of these approaches has been narrowly developed for a single substrate and cannot be easily extended to other protein substrates of interest. To address this shortcoming, we created a generalizable protein knock-out method by engineering protein chimeras called "ubiquibodies" that combine the activity of E3 ubiquitin ligases with designer binding proteins to steer virtually any protein to the UPP for degradation. Specifically, we reprogrammed the substrate specificity of a modular human E3 ubiquitin ligase called CHIP (carboxyl terminus of Hsc70-interacting protein) by replacing its natural substrate-binding domain with a single-chain Fv (scFv) intrabody or a fibronectin type III domain monobody that target their respective antigens with high specificity and affinity. Engineered ubiquibodies reliably transferred ubiquitin to surface exposed lysines on target proteins and even catalyzed the formation of biologically relevant polyubiquitin chains. Following ectopic expression of ubiquibodies in mammalian cells, specific and systematic depletion of desired target proteins was achieved, whereas the levels of a natural substrate of CHIP were unaffected. Taken together, engineered ubiquibodies offer a simple, reproducible, and customizable means for directly removing specific cellular proteins through accelerated proteolysis.
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48
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Merenbakh-Lamin K, Ben-Baruch N, Yeheskel A, Dvir A, Soussan-Gutman L, Jeselsohn R, Yelensky R, Brown M, Miller VA, Sarid D, Rizel S, Klein B, Rubinek T, Wolf I. D538G mutation in estrogen receptor-α: A novel mechanism for acquired endocrine resistance in breast cancer. Cancer Res 2013; 73:6856-64. [PMID: 24217577 DOI: 10.1158/0008-5472.can-13-1197] [Citation(s) in RCA: 300] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Resistance to endocrine therapy occurs in virtually all patients with estrogen receptor α (ERα)-positive metastatic breast cancer, and is attributed to various mechanisms including loss of ERα expression, altered activity of coregulators, and cross-talk between the ERα and growth factor signaling pathways. To our knowledge, acquired mutations of the ERα have not been described as mediating endocrine resistance. Samples of 13 patients with metastatic breast cancer were analyzed for mutations in cancer-related genes. In five patients who developed resistance to hormonal therapy, a mutation of A to G at position 1,613 of ERα, resulting in a substitution of aspartic acid at position 538 to glycine (D538G), was identified in liver metastases. Importantly, the mutation was not detected in the primary tumors obtained prior to endocrine treatment. Structural modeling indicated that D538G substitution leads to a conformational change in the ligand-binding domain, which mimics the conformation of activated ligand-bound receptor and alters binding of tamoxifen. Indeed, experiments in breast cancer cells indicated constitutive, ligand-independent transcriptional activity of the D538G receptor, and overexpression of it enhanced proliferation and conferred resistance to tamoxifen. These data indicate a novel mechanism of acquired endocrine resistance in breast cancer. Further studies are needed to assess the frequency of D538G-ERα among patients with breast cancer and explore ways to inhibit its activity and restore endocrine sensitivity.
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Affiliation(s)
- Keren Merenbakh-Lamin
- Authors' Affiliations: Department of Oncology, Tel Aviv Sourasky Medical Center; Sackler Faculty of Medicine; The Bioinformatics Unit, Goerge S. Wise Faculty of Life Sciences, Tel Aviv University; Assuta Medical Center, Tel Aviv; Kaplan Medical Center, Rehovot; Oncotest-Teva Pharmaceutical Industries; Institute of Oncology, Davidoff Center, Rabin Medical Center, Petach Tikva, Israel; Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; and Foundation Medicine, Cambridge, Massachusetts
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49
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Kovalenko OV, Olland A, Piché-Nicholas N, Godbole A, King D, Svenson K, Calabro V, Müller MR, Barelle CJ, Somers W, Gill DS, Mosyak L, Tchistiakova L. Atypical antigen recognition mode of a shark immunoglobulin new antigen receptor (IgNAR) variable domain characterized by humanization and structural analysis. J Biol Chem 2013; 288:17408-19. [PMID: 23632026 DOI: 10.1074/jbc.m112.435289] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The immunoglobulin new antigen receptors (IgNARs) are a class of Ig-like molecules of the shark immune system that exist as heavy chain-only homodimers and bind antigens by their single domain variable regions (V-NARs). Following shark immunization and/or in vitro selection, V-NARs can be generated as soluble, stable, and specific high affinity monomeric binding proteins of ∼12 kDa. We have previously isolated a V-NAR from an immunized spiny dogfish shark, named E06, that binds specifically and with high affinity to human, mouse, and rat serum albumins. Humanization of E06 was carried out by converting over 60% of non-complementarity-determining region residues to those of a human germ line Vκ1 sequence, DPK9. The resulting huE06 molecules have largely retained the specificity and affinity of antigen binding of the parental V-NAR. Crystal structures of the shark E06 and its humanized variant (huE06 v1.1) in complex with human serum albumin (HSA) were determined at 3- and 2.3-Å resolution, respectively. The huE06 v1.1 molecule retained all but one amino acid residues involved in the binding site for HSA. Structural analysis of these V-NARs has revealed an unusual variable domain-antigen interaction. E06 interacts with HSA in an atypical mode that utilizes extensive framework contacts in addition to complementarity-determining regions that has not been seen previously in V-NARs. On the basis of the structure, the roles of various elements of the molecule are described with respect to antigen binding and V-NAR stability. This information broadens the general understanding of antigen recognition and provides a framework for further design and humanization of shark IgNARs.
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Affiliation(s)
- Oleg V Kovalenko
- Global Biotherapeutics Technologies, Pfizer Research and Development, Cambridge, Massachusetts 02140, USA.
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50
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Gilbreth RN, Koide S. Structural insights for engineering binding proteins based on non-antibody scaffolds. Curr Opin Struct Biol 2012; 22:413-20. [PMID: 22749196 DOI: 10.1016/j.sbi.2012.06.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/25/2012] [Accepted: 06/01/2012] [Indexed: 11/18/2022]
Abstract
Engineered binding proteins derived from non-antibody scaffolds constitute an increasingly prominent class of reagents in both research and therapeutic applications. The growing number of crystal structures of these 'alternative' scaffold-based binding proteins in complex with their targets illustrate the mechanisms of molecular recognition that are common among these systems and those unique to each. This information is useful for critically assessing and improving/expanding engineering strategies. Furthermore, the structural features of these synthetic proteins produced under tightly controlled, directed evolution deepen our understanding of the underlying principles governing molecular recognition.
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Affiliation(s)
- Ryan N Gilbreth
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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