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Groza Y, Lacina L, Kuchař M, Rašková Kafková L, Zachová K, Janoušková O, Osička R, Černý J, Petroková H, Mierzwicka JM, Panova N, Kosztyu P, Sloupenská K, Malý J, Škarda J, Raška M, Smetana K, Malý P. Small protein blockers of human IL-6 receptor alpha inhibit proliferation and migration of cancer cells. Cell Commun Signal 2024; 22:261. [PMID: 38715108 PMCID: PMC11075285 DOI: 10.1186/s12964-024-01630-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Interleukin-6 (IL-6) is a multifunctional cytokine that controls the immune response, and its role has been described in the development of autoimmune diseases. Signaling via its cognate IL-6 receptor (IL-6R) complex is critical in tumor progression and, therefore, IL-6R represents an important therapeutic target. METHODS An albumin-binding domain-derived highly complex combinatorial library was used to select IL-6R alpha (IL-6Rα)-targeted small protein binders using ribosome display. Large-scale screening of bacterial lysates of individual clones was performed using ELISA, and their IL-6Rα blocking potential was verified by competition ELISA. The binding of proteins to cells was monitored by flow cytometry and confocal microscopy on HEK293T-transfected cells, and inhibition of signaling function was examined using HEK-Blue IL-6 reporter cells. Protein binding kinetics to living cells was measured by LigandTracer, cell proliferation and toxicity by iCELLigence and Incucyte, cell migration by the scratch wound healing assay, and prediction of binding poses using molecular modeling by docking. RESULTS We demonstrated a collection of protein variants called NEF ligands, selected from an albumin-binding domain scaffold-derived combinatorial library, and showed their binding specificity to human IL-6Rα and antagonistic effect in HEK-Blue IL-6 reporter cells. The three most promising NEF108, NEF163, and NEF172 variants inhibited cell proliferation of malignant melanoma (G361 and A2058) and pancreatic (PaTu and MiaPaCa) cancer cells, and suppressed migration of malignant melanoma (A2058), pancreatic carcinoma (PaTu), and glioblastoma (GAMG) cells in vitro. The NEF binders also recognized maturation-induced IL-6Rα expression and interfered with IL-6-induced differentiation in primary human B cells. CONCLUSION We report on the generation of small protein blockers of human IL-6Rα using directed evolution. NEF proteins represent a promising class of non-toxic anti-tumor agents with migrastatic potential.
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Affiliation(s)
- Yaroslava Groza
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Lukáš Lacina
- Institute of Anatomy, 1st Faculty of Medicine, Charles University, U Nemocnice 3, Prague 2, 12800, Czech Republic.
- Department of Dermatovenerology, 1st Faculty of Medicine, Charles University, U Nemocnice 2, Prague 2, 12000, Czech Republic.
| | - Milan Kuchař
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Leona Rašková Kafková
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 3, Olomouc, 779 00, Czech Republic
| | - Kateřina Zachová
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 3, Olomouc, 779 00, Czech Republic
| | - Olga Janoušková
- Centre of Nanomaterials and Biotechnologies, University of J. E. Purkyně in Ústí nad Labem, Pasteurova 3632/15, Ústí nad Labem, 400 96, Czech Republic
| | - Radim Osička
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic
| | - Jiří Černý
- Laboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Hana Petroková
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Joanna Maria Mierzwicka
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Natalya Panova
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Petr Kosztyu
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 3, Olomouc, 779 00, Czech Republic
| | - Kristýna Sloupenská
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 3, Olomouc, 779 00, Czech Republic
| | - Jan Malý
- Centre of Nanomaterials and Biotechnologies, University of J. E. Purkyně in Ústí nad Labem, Pasteurova 3632/15, Ústí nad Labem, 400 96, Czech Republic
| | - Jozef Škarda
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hněvotínská 3, Olomouc, 779 00, Czech Republic
| | - Milan Raška
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Hněvotínská 3, Olomouc, 779 00, Czech Republic
| | - Karel Smetana
- Institute of Anatomy, 1st Faculty of Medicine, Charles University, U Nemocnice 3, Prague 2, 12800, Czech Republic
| | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Prumyslova 595, Vestec, 252 50, Czech Republic.
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Zhihong Y, Chen W, Qianqian Z, Lidan S, Qiang Z, Jing H, Wenxi W, Bhawal R. Emerging roles of oxyntomodulin-based glucagon-like peptide-1/glucagon co-agonist analogs in diabetes and obesity. Peptides 2023; 162:170955. [PMID: 36669563 DOI: 10.1016/j.peptides.2023.170955] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
Oxyntomodulin (OXM) is an endogenous peptide hormone secreted from the intestines following nutrient ingestion that activates both glucagon-like peptide-1 (GLP-1) and glucagon receptors. OXM is known to exert various effects, including improvement in glucose tolerance, promotion of energy expenditure, acceleration of liver lipolysis, inhibition of food intake, delay of gastric emptying, neuroprotection, and pain relief. The antidiabetic and antiobesity properties have led to the development of biologically active and enzymatically stable OXM-based analogs with proposed therapeutic promise for metabolic diseases. Structural modification of OXM was ongoing to enhance its potency and prolong half-life, and several GLP-1/glucagon dual receptor agonist-based therapies are being explored in clinical trials for the treatment of type 2 diabetes mellitus and its complications. In the present article, we provide a brief overview of the physiology of OXM, focusing on its structural-activity relationship and ongoing clinical development.
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Affiliation(s)
- Yao Zhihong
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing 314001, China; College of Pharmacy, Zhejiang University of Technology, Hangzhou 310000, China
| | - Wang Chen
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing 314001, China
| | - Zhu Qianqian
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing 314001, China
| | - Sun Lidan
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing 314001, China.
| | - Zhou Qiang
- The First Hospital of Jiaxing & The Affiliated Hospital of Jiaxing University, Jiaxing 314001, China.
| | - Han Jing
- School of Chemistry & Materials Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Wang Wenxi
- The First Hospital of Jiaxing & The Affiliated Hospital of Jiaxing University, Jiaxing 314001, China; College of Pharmacy, Zhejiang University of Technology, Hangzhou 310000, China
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
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Luo R, Liu H, Cheng Z. Protein scaffolds: Antibody alternative for cancer diagnosis and therapy. RSC Chem Biol 2022; 3:830-847. [PMID: 35866165 PMCID: PMC9257619 DOI: 10.1039/d2cb00094f] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/23/2022] [Indexed: 12/01/2022] Open
Abstract
Although antibodies are well developed and widely used in cancer therapy and diagnostic fields, some defects remain, such as poor tissue penetration, long in vivo metabolic retention, potential cytotoxicity, patent limitation, and high production cost. These issues have led scientists to explore and develop novel antibody alternatives. Protein scaffolds are small monomeric proteins with stable tertiary structures and mutable residues, which emerged in the 1990s. By combining robust gene engineering and phage display techniques, libraries with sufficient diversity could be established for target binding scaffold selection. Given the properties of small size, high affinity, and excellent specificity and stability, protein scaffolds have been applied in basic research, and preclinical and clinical fields over the past two decades. To date, more than 20 types of protein scaffolds have been developed, with the most frequently used being affibody, adnectin, ANTICALIN®, DARPins, and knottin. In this review, we focus on the protein scaffold applications in cancer therapy and diagnosis in the last 5 years, and discuss the pros and cons, and strategies of optimization and design. Although antibodies are well developed and widely used in cancer therapy and diagnostic fields, some defects remain, such as poor tissue penetration, long in vivo metabolic retention, potential cytotoxicity, patent limitation, and high production cost.![]()
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Affiliation(s)
- Renli Luo
- Department of Molecular Medicine, College of Life and Health Sciences, Northeastern University Shenyang China
| | - Hongguang Liu
- Department of Molecular Medicine, College of Life and Health Sciences, Northeastern University Shenyang China
| | - Zhen Cheng
- State Key Laboratory of Drug Research, Molecular Imaging Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- Drug Discovery Shandong Laboratory, Bohai Rim Advanced Research Institute for Drug Discovery Yantai Shandong 264117 China
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Ito T, Nishi H, Kameda T, Yoshida M, Fukazawa R, Kawada S, Nakazawa H, Umetsu M. Combination Informatic and Experimental Approach for Selecting Scaffold Proteins for Development as Antibody Mimetics. CHEM LETT 2021. [DOI: 10.1246/cl.210443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomoyuki Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Hafumi Nishi
- Department of Applied Information Sciences, Graduate School of Information Science, Tohoku University, 6-3-09 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Faculty of Core Research, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Mayu Yoshida
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Reito Fukazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Sakiya Kawada
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
- Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
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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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Pham PN, Huličiak M, Biedermannová L, Černý J, Charnavets T, Fuertes G, Herynek Š, Kolářová L, Kolenko P, Pavlíček J, Zahradník J, Mikulecky P, Schneider B. Protein Binder (ProBi) as a New Class of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution. Viruses 2021; 13:v13020190. [PMID: 33514045 PMCID: PMC7911045 DOI: 10.3390/v13020190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/15/2021] [Accepted: 01/23/2021] [Indexed: 12/13/2022] Open
Abstract
Engineered small non-antibody protein scaffolds are a promising alternative to antibodies and are especially attractive for use in protein therapeutics and diagnostics. The advantages include smaller size and a more robust, single-domain structural framework with a defined binding surface amenable to mutation. This calls for a more systematic approach in designing new scaffolds suitable for use in one or more methods of directed evolution. We hereby describe a process based on an analysis of protein structures from the Protein Data Bank and their experimental examination. The candidate protein scaffolds were subjected to a thorough screening including computational evaluation of the mutability, and experimental determination of their expression yield in E. coli, solubility, and thermostability. In the next step, we examined several variants of the candidate scaffolds including their wild types and alanine mutants. We proved the applicability of this systematic procedure by selecting a monomeric single-domain human protein with a fold different from previously known scaffolds. The newly developed scaffold, called ProBi (Protein Binder), contains two independently mutable surface patches. We demonstrated its functionality by training it as a binder against human interleukin-10, a medically important cytokine. The procedure yielded scaffold-related variants with nanomolar affinity.
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Huang P, Meng L, Tan J, Gu X, Huang M, Huang F, Ma R, Wang J. S3-2, a novel long-lasting oxyntomodulin derivative, exerts improvement on diabesity and renal injury through activating GLP-1 and glucagon receptors. Life Sci 2021; 270:119136. [PMID: 33508289 DOI: 10.1016/j.lfs.2021.119136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
AIMS To prolong the short lifespan of oxyntomodulin (OXM) for treating obesity and diabetes, we designed a novel fused OXM analog, containing an albumin-binding sequence, a protease cleavable tetrapeptide, and a mutated OXM. MAIN METHODS We screened two albumin-binding sequences (S3 and S6) to construct OXM derivatives, termed S3-2 (with two cysteines) and S6-0 (without cysteine). After peptides were synthesized, isothermal titration calorimetry (ITC) was applied to assess binding-affinity for HSA. Further in vivo acute efficacies evaluation and candidate selection were performed in diabetic db/db mice via oral glucose tolerance test (OGTT) and glucose-lowering duration test. Chronic efficacy test of selected candidate was also performed in diabetic mice. RESULTS Firstly, S3-2 and S6-0 with purity over 99% were prepared. ITC measurements demonstrated that S3-2 and S6-0 associate with HSA with high-affinity (Kd = 12.81 ± 1.11 nM and 26.98 ± 2.39 nM, respectively). Then hypoglycemic efficacies showed deoxidation S3-2 (S3-2re) showed longer hypoglycemic duration than the oxidation one (S3-2ox), and better blood glucose level (BGL) control effect than S6-0. OGTTs in diabetic mice revealed the glucose-lowering efficacies of S3-2re were similar to Liraglutide. The protracted antidiabetic effects of S3-2re were further confirmed by multiple OGTTs in db/db mice. Furthermore, twice weekly injection of S3-2re to db/db mice achieved beneficial effects on body weight gain, glucose tolerance, postprandial BGL and obesity. Moreover, S3-2 produces significantly protective effects on the impaired renal functions of the diabetic mice. CONCLUSION S3-2re exhibits outstanding therapeutical potential as a candidate drug for treating the obesity and diabetes.
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Affiliation(s)
- Peng Huang
- Department of Nephrology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 53300, Guangxi, PR China
| | - Lingzhang Meng
- Center for Systemic Inflammation Research, School of Preclinical Medicine, Youjiang Medical University for Nationalities, Baise 53300, Guangxi, PR China
| | - Junhua Tan
- Department of Nephrology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 53300, Guangxi, PR China
| | - Xianjun Gu
- Department of Nephrology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 53300, Guangxi, PR China
| | - Meiying Huang
- Department of Nephrology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 53300, Guangxi, PR China
| | - Feifan Huang
- Department of Nephrology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 53300, Guangxi, PR China
| | - Ruiying Ma
- Department of Nephrology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 53300, Guangxi, PR China
| | - Jie Wang
- Department of Nephrology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 53300, Guangxi, PR China.
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Cell immunocapture microfluidic chip based on high-affinity recombinant protein binders. Biosens Bioelectron 2021; 172:112784. [PMID: 33161292 DOI: 10.1016/j.bios.2020.112784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/30/2020] [Accepted: 10/30/2020] [Indexed: 12/29/2022]
Abstract
Cell immunocapture microfluidic devices represent a rapidly developing field with many potential applications in medical diagnostics. The core of such approach lies in the cell binding to antibody coated surfaces through their surface receptors. Here we show, that the small recombinant protein binders (PBs) can be used for this purpose as well, with the advantage of their constructional flexibility, possibility of fusion with range of tags and cheap mass production. For this purpose, two different PBs derived from Albumin Binding Domain (ABDwt) of streptococcal protein G, so called REX and ARS ligands with proved high affinity and selectivity to the human interleukin-23 (IL-23R) and IL-17 receptor A were used. Four PBs variants recognizing two different epitopes on two different receptors and two PBs variants binding to the same epitope on one receptor but having different peptide spacer with Avitag sequence necessary for their immobilization on sensor surface were tested for cell-capture efficiency. The glass microfluidic Y-system with planar immunocapture channel working in so-called stop-flow dynamic regime was designed. Up to 60-74% immunocapture efficiency of model THP-1 cells on REX/ARS surfaces and practically no cell binding on control ABDwt surfaces was achieved. Moreover, the specific immunocapture of THP-1 cells from mixture with IL-17RA negative DU-145 cells was demonstrated. We discuss the role of the epitope, affinity and immobilization spacer of PBs as well as the influence of stop-flow dynamic regime on the effectivity of THP-1 cell immunocapture. Results can be further exploited in design of microfluidic devices for rare cells immunocapture.
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Proteins mimicking epitope of HIV-1 virus neutralizing antibody induce virus-neutralizing sera in mice. EBioMedicine 2020; 47:247-256. [PMID: 31544770 PMCID: PMC6796546 DOI: 10.1016/j.ebiom.2019.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/28/2019] [Accepted: 07/04/2019] [Indexed: 01/26/2023] Open
Abstract
Background The development of an effective vaccine preventing HIV-1 infection is hindered by the enormous antigenic variability and unique biochemical and immunological properties of HIV-1 Env glycoprotein, the most promising target for HIV-1 neutralizing antibody. Functional studies of rare elite neutralizers led to the discovery of broadly neutralizing antibodies. Methods We employed a highly complex combinatorial protein library derived from a 5 kDa albumin-binding domain scaffold, fused with support protein of total 38 kDa, to screen for binders of broadly neutralizing antibody VRC01 paratope. The most specific binders were used for immunization of experimental mice to elicit Env-specific antibodies and to test their neutralization activity using a panel of HIV-1 clade C and B pseudoviruses. Findings Three most specific binders designated as VRA017, VRA019, and VRA177 exhibited high specificity to VRC01 antibody. Immunized mice produced Env-binding antibodies which neutralize eight of twelve HIV-1 Tier 2 pseudoviruses. Molecular modelling revealed a shape complementarity between VRA proteins and a part of VRC01 gp120 interacting surface. Interpretation This strategy based on the identification of protein replicas of broadly neutralizing antibody paratope represents a novel approach in HIV-1 vaccine development. This approach is not affected by low immunogenicity of neutralization-sensitive epitopes, variability, and unique biochemical properties of HIV-1 Env used as a crucial antigen in the majority of contemporary tested vaccines. Fund Czech Health Research Council 15-32198A, Ministry of Health, Czech Republic.
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Petroková H, Mašek J, Kuchař M, Vítečková Wünschová A, Štikarová J, Bartheldyová E, Kulich P, Hubatka F, Kotouček J, Turánek Knotigová P, Vohlídalová E, Héžová R, Mašková E, Macaulay S, Dyr JE, Raška M, Mikulík R, Malý P, Turánek J. Targeting Human Thrombus by Liposomes Modified with Anti-Fibrin Protein Binders. Pharmaceutics 2019; 11:pharmaceutics11120642. [PMID: 31810280 PMCID: PMC6955937 DOI: 10.3390/pharmaceutics11120642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022] Open
Abstract
Development of tools for direct thrombus imaging represents a key step for diagnosis and treatment of stroke. Nanoliposomal carriers of contrast agents and thrombolytics can be functionalized to target blood thrombi by small protein binders with selectivity for fibrin domains uniquely formed on insoluble fibrin. We employed a highly complex combinatorial library derived from scaffold of 46 amino acid albumin-binding domain (ABD) of streptococcal protein G, and ribosome display, to identify variants recognizing fibrin cloth in human thrombus. We constructed a recombinant target as a stretch of three identical fibrin fragments of 16 amino acid peptide of the Bβ chain fused to TolA protein. Ribosome display selection followed by large-scale Enzyme-Linked ImmunoSorbent Assay (ELISA) screening provided four protein variants preferentially binding to insoluble form of human fibrin. The most specific binder variant D7 was further modified by C-terminal FLAG/His-Tag or double His-tag for the attachment onto the surface of nanoliposomes via metallochelating bond. D7-His-nanoliposomes were tested using in vitro flow model of coronary artery and their binding to fibrin fibers was demonstrated by confocal and electron microscopy. Thus, we present here the concept of fibrin-targeted binders as a platform for functionalization of nanoliposomes in the development of advanced imaging tools and future theranostics.
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Affiliation(s)
- Hana Petroková
- Laboratory of Ligand Engineering, Institute of Biotechnology, Czech Academy of Sciences, v.v.i., BIOCEV Research Center, Průmyslová 595, 252 50 Vestec, Czech Republic; (H.P.); (M.K.)
| | - Josef Mašek
- Department of Pharmacology and Immunotherapy, Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic; (J.M.); (A.V.W.); (E.B.); (P.K.); (F.H.); (J.K.); (P.T.K.); (E.V.); (R.H.); (E.M.)
| | - Milan Kuchař
- Laboratory of Ligand Engineering, Institute of Biotechnology, Czech Academy of Sciences, v.v.i., BIOCEV Research Center, Průmyslová 595, 252 50 Vestec, Czech Republic; (H.P.); (M.K.)
| | - Andrea Vítečková Wünschová
- Department of Pharmacology and Immunotherapy, Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic; (J.M.); (A.V.W.); (E.B.); (P.K.); (F.H.); (J.K.); (P.T.K.); (E.V.); (R.H.); (E.M.)
| | - Jana Štikarová
- Department of Biochemistry, Institute of Hematology and Blood Transfusion, U nemocnice 2094/1, 128 20 Praha 2, Czech Republic; (J.Š.); (J.E.D.)
| | - Eliška Bartheldyová
- Department of Pharmacology and Immunotherapy, Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic; (J.M.); (A.V.W.); (E.B.); (P.K.); (F.H.); (J.K.); (P.T.K.); (E.V.); (R.H.); (E.M.)
| | - Pavel Kulich
- Department of Pharmacology and Immunotherapy, Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic; (J.M.); (A.V.W.); (E.B.); (P.K.); (F.H.); (J.K.); (P.T.K.); (E.V.); (R.H.); (E.M.)
| | - František Hubatka
- Department of Pharmacology and Immunotherapy, Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic; (J.M.); (A.V.W.); (E.B.); (P.K.); (F.H.); (J.K.); (P.T.K.); (E.V.); (R.H.); (E.M.)
| | - Jan Kotouček
- Department of Pharmacology and Immunotherapy, Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic; (J.M.); (A.V.W.); (E.B.); (P.K.); (F.H.); (J.K.); (P.T.K.); (E.V.); (R.H.); (E.M.)
| | - Pavlína Turánek Knotigová
- Department of Pharmacology and Immunotherapy, Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic; (J.M.); (A.V.W.); (E.B.); (P.K.); (F.H.); (J.K.); (P.T.K.); (E.V.); (R.H.); (E.M.)
| | - Eva Vohlídalová
- Department of Pharmacology and Immunotherapy, Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic; (J.M.); (A.V.W.); (E.B.); (P.K.); (F.H.); (J.K.); (P.T.K.); (E.V.); (R.H.); (E.M.)
| | - Renata Héžová
- Department of Pharmacology and Immunotherapy, Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic; (J.M.); (A.V.W.); (E.B.); (P.K.); (F.H.); (J.K.); (P.T.K.); (E.V.); (R.H.); (E.M.)
| | - Eliška Mašková
- Department of Pharmacology and Immunotherapy, Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic; (J.M.); (A.V.W.); (E.B.); (P.K.); (F.H.); (J.K.); (P.T.K.); (E.V.); (R.H.); (E.M.)
| | - Stuart Macaulay
- Malvern Instruments Ltd., Enigma Business Park, Grove Lane, Malvern WR14 1XZ, UK;
| | - Jan Evangelista Dyr
- Department of Biochemistry, Institute of Hematology and Blood Transfusion, U nemocnice 2094/1, 128 20 Praha 2, Czech Republic; (J.Š.); (J.E.D.)
| | - Milan Raška
- Department of Pharmacology and Immunotherapy, Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic; (J.M.); (A.V.W.); (E.B.); (P.K.); (F.H.); (J.K.); (P.T.K.); (E.V.); (R.H.); (E.M.)
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hněvotínská 3, 775 15 Olomouc, Czech Republic
| | - Robert Mikulík
- The International Clinical Research Center ICRC and Neurology Department of St. Anne’s University Hospital in Brno, Pekařská 53, 656 91 Brno, Czech Republic;
| | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology, Czech Academy of Sciences, v.v.i., BIOCEV Research Center, Průmyslová 595, 252 50 Vestec, Czech Republic; (H.P.); (M.K.)
- Correspondence: (P.M.); (J.T.); Tel.: +420-325-873-763 (P.M.); +420-732-813-577 (J.T.)
| | - Jaroslav Turánek
- Department of Pharmacology and Immunotherapy, Veterinary Research Institute, v.v.i., Hudcova 70, 621 00 Brno, Czech Republic; (J.M.); (A.V.W.); (E.B.); (P.K.); (F.H.); (J.K.); (P.T.K.); (E.V.); (R.H.); (E.M.)
- Correspondence: (P.M.); (J.T.); Tel.: +420-325-873-763 (P.M.); +420-732-813-577 (J.T.)
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Engineered Lactococcus lactis Secreting IL-23 Receptor-Targeted REX Protein Blockers for Modulation of IL-23/Th17-Mediated Inflammation. Microorganisms 2019; 7:microorganisms7050152. [PMID: 31137908 PMCID: PMC6560508 DOI: 10.3390/microorganisms7050152] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/09/2019] [Accepted: 05/23/2019] [Indexed: 12/13/2022] Open
Abstract
Lactococcus lactis, a probiotic bacterium of food origin, has recently been demonstrated as a suitable strain for the production and in vivo delivery of therapeutically important proteins into the gut. We aimed to engineer recombinant L. lactis cells producing/secreting REX binding proteins that have been described as IL-23 receptor (IL-23R) blockers and IL-23R antagonists suppressing the secretion of cytokine IL-17A, a pivotal step in the T-helper Th17-mediated pro-inflammatory cascade, as well as in the development of autoimmune diseases, including inflammatory bowel disease (IBD). To reach this goal, we introduced cDNA sequences coding for REX009, REX115, and REX125 proteins into plasmid vectors carrying a Usp45 secretion signal, a FLAG tag sequence consensus, and a LysM-containing cA surface anchor (AcmA), thus allowing cell-surface peptidoglycan anchoring. These plasmids, or their non-FLAG/non-AcmA versions, were introduced into L. lactis host cells, thus generating unique recombinant L. lactis-REX strains. We demonstrate that all three REX proteins are expressed in L. lactis cells and are efficiently displayed on the bacterial surface, as tested by flow cytometry using an anti-FLAG antibody conjugate. Upon 10-fold concentration of the conditioned media, a REX125 secretory variant can be detected by Western blotting. To confirm that the FLAG/non-FLAG REX proteins displayed by L. lactis retain their binding specificity, cell-surface interactions of REX proteins with an IL-23R-IgG chimera were demonstrated by flow cytometry. In addition, statistically significant binding of secreted REX009 and REX115 proteins to bacterially produced, soluble human IL-23R was confirmed by ELISA. We conclude that REX-secreting L. lactis strains were engineered that might serve as IL-23/IL-23R blockers in an experimentally induced mouse model of colitis.
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Hober S, Lindbo S, Nilvebrant J. Bispecific applications of non-immunoglobulin scaffold binders. Methods 2019; 154:143-152. [DOI: 10.1016/j.ymeth.2018.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/24/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
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ABD-Derived Protein Blockers of Human IL-17 Receptor A as Non-IgG Alternatives for Modulation of IL-17-Dependent Pro-Inflammatory Axis. Int J Mol Sci 2018; 19:ijms19103089. [PMID: 30304852 PMCID: PMC6213189 DOI: 10.3390/ijms19103089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/04/2018] [Accepted: 10/06/2018] [Indexed: 12/14/2022] Open
Abstract
Interleukin 17 (IL-17) and its cognate receptor A (IL-17RA) play a crucial role in Th17 cells-mediated pro-inflammatory pathway and pathogenesis of several autoimmune disorders including psoriasis. IL-17 is mainly produced by activated Th-17 helper cells upon stimulation by IL-23 and, via binding to its receptors, mediates IL-17-driven cell signaling in keratinocytes. Hyper-proliferation of keratinocytes belongs to major clinical manifestations in psoriasis. To modulate IL-17-mediated inflammatory cascade, we generated a unique collection of IL-17RA-targeting protein binders that prevent from binding of human IL-17A cytokine to its cell-surface receptor. To this goal, we used a highly complex combinatorial library derived from scaffold of albumin-binding domain (ABD) of streptococcal protein G, and ribosome display selection, to yield a collection of ABD-derived high-affinity ligands of human IL-17RA, called ARS binders. From 67 analyzed ABD variants, 7 different sequence families were identified. Representatives of these groups competed with human IL-17A for binding to recombinant IL-17RA receptor as well as to IL-17RA-Immunoglobulin G chimera, as tested in enzyme-linked immunosorbent assay (ELISA). Five ARS variants bound to IL-17RA-expressing THP-1 cells and blocked binding of human IL-17 cytokine to the cell surface, as tested by flow cytometry. Three variants exhibited high-affinity binding with a nanomolar Kd value to human keratinocyte HaCaT cells, as measured using Ligand Tracer Green Line. Upon IL-17-stimulated activation, ARS variants inhibited secretion of Gro-α (CXCL1) by normal human skin fibroblasts in vitro. Thus, we identified a novel class of inhibitory ligands that might serve as immunosuppressive IL-17RA-targeted non-IgG protein antagonists.
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p19-Targeting ILP Protein Blockers of IL-23/Th-17 Pro-Inflammatory Axis Displayed on Engineered Bacteria of Food Origin. Int J Mol Sci 2018; 19:ijms19071933. [PMID: 29966384 PMCID: PMC6073689 DOI: 10.3390/ijms19071933] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/23/2018] [Accepted: 06/29/2018] [Indexed: 12/31/2022] Open
Abstract
IL-23-mediated Th-17 cell activation and stimulation of IL-17-driven pro-inflammatory axis has been associated with autoimmunity disorders such as Inflammatory Bowel Disease (IBD) or Crohn’s Disease (CD). Recently we developed a unique class of IL-23-specific protein blockers, called ILP binding proteins that inhibit binding of IL-23 to its cognate cell-surface receptor (IL-23R) and exhibit immunosuppressive effect on human primary blood leukocytes ex vivo. In this study, we aimed to generate a recombinant Lactococcus lactis strain which could serve as in vivo producer/secretor of IL-23 protein blockers into the gut. To achieve this goal, we introduced ILP030, ILP317 and ILP323 cDNA sequences into expression plasmid vector containing USP45 secretion signal, FLAG sequence consensus and LysM-containing cA surface anchor (AcmA) ensuring cell-surface peptidoglycan anchoring. We demonstrate that all ILP variants are expressed in L. lactis cells, efficiently transported and secreted from the cell and displayed on the bacterial surface. The binding function of AcmA-immobilized ILP proteins is documented by interaction with a recombinant p19 protein, alpha subunit of human IL-23, which was assembled in the form of a fusion with Thioredoxin A. ILP317 variant exhibits the best binding to the human IL-23 cytokine, as demonstrated for particular L.lactis-ILP recombinant variants by Enzyme-Linked ImmunoSorbent Assay (ELISA). We conclude that novel recombinant ILP-secreting L. lactis strains were developed that might be useful for further in vivo studies of IL-23-mediated inflammation on animal model of experimentally-induced colitis.
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Semerádtová A, Štofik M, Neděla O, Staněk O, Slepička P, Kolská Z, Malý J. A simple approach for fabrication of optical affinity-based bioanalytical microsystem on polymeric PEN foils. Colloids Surf B Biointerfaces 2018; 165:28-36. [DOI: 10.1016/j.colsurfb.2018.01.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 12/20/2022]
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16
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Emerging Cytokine Biosensors with Optical Detection Modalities and Nanomaterial-Enabled Signal Enhancement. SENSORS 2017; 17:s17020428. [PMID: 28241443 PMCID: PMC5335944 DOI: 10.3390/s17020428] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/12/2017] [Accepted: 02/18/2017] [Indexed: 12/17/2022]
Abstract
Protein biomarkers, especially cytokines, play a pivotal role in the diagnosis and treatment of a wide spectrum of diseases. Therefore, a critical need for advanced cytokine sensors has been rapidly growing and will continue to expand to promote clinical testing, new biomarker development, and disease studies. In particular, sensors employing transduction principles of various optical modalities have emerged as the most common means of detection. In typical cytokine assays which are based on the binding affinities between the analytes of cytokines and their specific antibodies, optical schemes represent the most widely used mechanisms, with some serving as the gold standard against which all existing and new sensors are benchmarked. With recent advancements in nanoscience and nanotechnology, many of the recently emerging technologies for cytokine detection exploit various forms of nanomaterials for improved sensing capabilities. Nanomaterials have been demonstrated to exhibit exceptional optical properties unique to their reduced dimensionality. Novel sensing approaches based on the newly identified properties of nanomaterials have shown drastically improved performances in both the qualitative and quantitative analyses of cytokines. This article brings together the fundamentals in the literature that are central to different optical modalities developed for cytokine detection. Recent advancements in the applications of novel technologies are also discussed in terms of those that enable highly sensitive and multiplexed cytokine quantification spanning a wide dynamic range. For each highlighted optical technique, its current detection capabilities as well as associated challenges are discussed. Lastly, an outlook for nanomaterial-based cytokine sensors is provided from the perspective of optimizing the technologies for sensitivity and multiplexity as well as promoting widespread adaptations of the emerging optical techniques by lowering high thresholds currently present in the new approaches.
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Křížová L, Kuchař M, Petroková H, Osička R, Hlavničková M, Pelák O, Černý J, Kalina T, Malý P. p19-targeted ABD-derived protein variants inhibit IL-23 binding and exert suppressive control over IL-23-stimulated expansion of primary human IL-17+ T-cells. Autoimmunity 2017; 50:102-113. [DOI: 10.1080/08916934.2016.1272598] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lucie Křížová
- Laboratory of Ligand Engineering, Institute of Biotechnology, Czech Academy of Sciences, v. v. i, BIOCEV Research Center, Vestec, Czech Republic,
| | - Milan Kuchař
- Laboratory of Ligand Engineering, Institute of Biotechnology, Czech Academy of Sciences, v. v. i, BIOCEV Research Center, Vestec, Czech Republic,
| | - Hana Petroková
- Laboratory of Ligand Engineering, Institute of Biotechnology, Czech Academy of Sciences, v. v. i, BIOCEV Research Center, Vestec, Czech Republic,
| | - Radim Osička
- Laboratory of Molecular Biology of the Bacterial Pathogens, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic,
| | - Marie Hlavničková
- Laboratory of Ligand Engineering, Institute of Biotechnology, Czech Academy of Sciences, v. v. i, BIOCEV Research Center, Vestec, Czech Republic,
| | - Ondřej Pelák
- CLIP, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic, and
| | - Jiří Černý
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, Czech Academy of Sciences, v. v. i, BIOCEV Research Center, Vestec, Czech Republic
| | - Tomáš Kalina
- CLIP, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic, and
| | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology, Czech Academy of Sciences, v. v. i, BIOCEV Research Center, Vestec, Czech Republic,
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18
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Zadravec P, Marečková L, Petroková H, Hodnik V, Perišić Nanut M, Anderluh G, Štrukelj B, Malý P, Berlec A. Development of Recombinant Lactococcus lactis Displaying Albumin-Binding Domain Variants against Shiga Toxin 1 B Subunit. PLoS One 2016; 11:e0162625. [PMID: 27606705 PMCID: PMC5015993 DOI: 10.1371/journal.pone.0162625] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/25/2016] [Indexed: 01/06/2023] Open
Abstract
Infections with shiga toxin-producing bacteria, like enterohemorrhagic Escherichia coli and Shigella dysenteriae, represent a serious medical problem. No specific and effective treatment is available for patients with these infections, creating a need for the development of new therapies. Recombinant lactic acid bacterium Lactococcus lactis was engineered to bind Shiga toxin by displaying novel designed albumin binding domains (ABD) against Shiga toxin 1 B subunit (Stx1B) on their surface. Functional recombinant Stx1B was produced in Escherichia coli and used as a target for selection of 17 different ABD variants (named S1B) from the ABD scaffold-derived high-complex combinatorial library in combination with a five-round ribosome display. Two most promising S1Bs (S1B22 and S1B26) were characterized into more details by ELISA, surface plasmon resonance and microscale thermophoresis. Addition of S1Bs changed the subcellular distribution of Stx1B, completely eliminating it from Golgi apparatus most likely by interfering with its retrograde transport. All ABD variants were successfully displayed on the surface of L. lactis by fusing to the Usp45 secretion signal and to the peptidoglycan-binding C terminus of AcmA. Binding of Stx1B by engineered lactococcal cells was confirmed using flow cytometry and whole cell ELISA. Lactic acid bacteria prepared in this study are potentially useful for the removal of Shiga toxin from human intestine.
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Affiliation(s)
- Petra Zadravec
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- The Chair of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000, Ljubljana, Slovenia
| | - Lucie Marečková
- Laboratory of Ligand Engineering, Institute of Biotechnology CAS, v. v. i., BIOCEV Research Center, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Hana Petroková
- Laboratory of Ligand Engineering, Institute of Biotechnology CAS, v. v. i., BIOCEV Research Center, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Vesna Hodnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Milica Perišić Nanut
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Borut Štrukelj
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- The Chair of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000, Ljubljana, Slovenia
| | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology CAS, v. v. i., BIOCEV Research Center, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Aleš Berlec
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000, Ljubljana, Slovenia
- * E-mail:
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Novel binders derived from an albumin-binding domain scaffold targeting human prostate secretory protein 94 (PSP94). Protein Cell 2016; 6:774-9. [PMID: 26264490 PMCID: PMC4598320 DOI: 10.1007/s13238-015-0194-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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20
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Islam MA, Bhayye S, Adeniyi AA, Soliman ME, Pillay TS. Diabetes mellitus caused by mutations in human insulin: analysis of impaired receptor binding of insulins Wakayama, Los Angeles and Chicago using pharmacoinformatics. J Biomol Struct Dyn 2016; 35:724-737. [DOI: 10.1080/07391102.2016.1160258] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Md Ataul Islam
- Faculty of Health Sciences, Department of Chemical Pathology, & Institute of Cellular & Molecular Medicine, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Pretoria, South Africa
| | - Sagar Bhayye
- Department of Chemical Technology, University of Calcutta, 92, A. P. C. Road, Kolkata 700009, India
| | - Adebayo A. Adeniyi
- Discipline of Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Mahmoud E.S. Soliman
- Discipline of Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Tahir S. Pillay
- Faculty of Health Sciences, Department of Chemical Pathology, & Institute of Cellular & Molecular Medicine, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Pretoria, South Africa
- Division of Chemical Pathology, University of Cape Town, Cape Town, South Africa
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Maly J, Stanek O, Frolik J, Maly M, Ennen F, Appelhans D, Semeradtova A, Wrobel D, Stofik M, Knapova T, Kuchar M, Stastna LC, Cermak J, Sebo P, Maly P. Biocompatible Size-Defined Dendrimer-Albumin Binding Protein Hybrid Materials as a Versatile Platform for Biomedical Applications. Macromol Biosci 2016; 16:553-66. [PMID: 26748571 DOI: 10.1002/mabi.201500332] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/23/2015] [Indexed: 12/14/2022]
Abstract
For the design of a biohybrid structure as a ligand-tailored drug delivery system (DDS), it is highly sophisticated to fabricate a DDS based on smoothly controllable conjugation steps. This article reports on the synthesis and the characterization of biohybrid conjugates based on noncovalent conjugation between a multivalent biotinylated and PEGylated poly(amido amine) (PAMAM) dendrimer and a tetrameric streptavidin-small protein binding scaffold. This protein binding scaffold (SA-ABDwt) possesses nM affinity toward human serum albumin (HSA). Thus, well-defined biohybrid structures, finalized by binding of one or two HSA molecules, are available at each conjugation step in a controlled molar ratio. Overall, these biohybrid assemblies can be used for (i) a controlled modification of dendrimers with the HSA molecules to increase their blood-circulation half-life and passive accumulation in tumor; (ii) rendering dendrimers a specific affinity to various ligands based on mutated ABD domain, thus replacing tedious dendrimer-antibody covalent coupling and purification procedures.
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Affiliation(s)
- Jan Maly
- Department of Biology, Faculty of Science, University of J.E. Purkinje, 400 96, Ústí nad Labem, Czech Republic
| | - Ondrej Stanek
- Institute of Biotechnology CAS, v. v. i, Pru˚myslová 595, Vestec, ,252 42, Jesenice u Prahy, Czech Republic
| | - Jan Frolik
- Department of Biology, Faculty of Science, University of J.E. Purkinje, 400 96, Ústí nad Labem, Czech Republic
| | - Marek Maly
- Department of Biology, Faculty of Science, University of J.E. Purkinje, 400 96, Ústí nad Labem, Czech Republic
| | - Franka Ennen
- Leibniz Institute of Polymer Research Dresden, Hohe Straße 6, D-01069, Dresden, Germany
| | - Dietmar Appelhans
- Leibniz Institute of Polymer Research Dresden, Hohe Straße 6, D-01069, Dresden, Germany
| | - Alena Semeradtova
- Department of Biology, Faculty of Science, University of J.E. Purkinje, 400 96, Ústí nad Labem, Czech Republic
| | - Dominika Wrobel
- Department of Biology, Faculty of Science, University of J.E. Purkinje, 400 96, Ústí nad Labem, Czech Republic
| | - Marcel Stofik
- Department of Biology, Faculty of Science, University of J.E. Purkinje, 400 96, Ústí nad Labem, Czech Republic
| | - Tereza Knapova
- Department of Biology, Faculty of Science, University of J.E. Purkinje, 400 96, Ústí nad Labem, Czech Republic
| | - Milan Kuchar
- Institute of Biotechnology CAS, v. v. i, Pru˚myslová 595, Vestec, ,252 42, Jesenice u Prahy, Czech Republic
| | - Lucie Cervenkova Stastna
- Institute of Chemical Process Fundamentals CAS, v. v. i, Rozvojová 135, 165 02, Prague, Czech Republic
| | - Jan Cermak
- Institute of Chemical Process Fundamentals CAS, v. v. i, Rozvojová 135, 165 02, Prague, Czech Republic
| | - Peter Sebo
- Institute of Microbiology CAS, v. v. i, Vídeˇnská 1083, 142 20, Prague, Czech Republic
| | - Petr Maly
- Institute of Biotechnology CAS, v. v. i, Pru˚myslová 595, Vestec, ,252 42, Jesenice u Prahy, Czech Republic
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Abstract
Detection of desired target chemicals in a sensitive and selective manner is critically important to protect human health, environment and national security. Nature has been a great source of inspiration for the design of sensitive and selective sensors. In this mini-review, we overview the recent developments in bio-inspired sensor development. There are four major components of sensor design: design of receptors for specific targets; coating materials to integrate receptors to transducing machinery; sensitive transducing of signals; and decision making based on the sensing results. We discuss the biomimetic methods to discover specific receptors followed by a discussion about bio-inspired nanocoating material design. We then review the recent developments in phage-based bioinspired transducing systems followed by a discussion of biomimetic pattern recognition-based decision making systems. Our review will be helpful to understand recent approaches to reverse-engineer natural systems to design specific and sensitive sensors.
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Affiliation(s)
- Ju Hun Lee
- Department of Bioengineering, University of California, Berkeley, USA.
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Kuchař M, Vaňková L, Petroková H, Cerný J, Osička R, Pelák O, Sípová H, Schneider B, Homola J, Sebo P, Kalina T, Malý P. Human interleukin-23 receptor antagonists derived from an albumin-binding domain scaffold inhibit IL-23-dependent ex vivo expansion of IL-17-producing T-cells. Proteins 2013; 82:975-89. [PMID: 24549990 PMCID: PMC4285857 DOI: 10.1002/prot.24472] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 10/30/2013] [Accepted: 11/04/2013] [Indexed: 12/12/2022]
Abstract
Engineered combinatorial libraries derived from small protein scaffolds represent a powerful tool for generating novel binders with high affinity, required specificity and designed inhibitory function. This work was aimed to generate a collection of recombinant binders of human interleukin-23 receptor (IL-23R), which is a key element of proinflammatory IL-23-mediated signaling. A library of variants derived from the three-helix bundle scaffold of the albumin-binding domain (ABD) of streptococcal protein G and ribosome display were used to select for high-affinity binders of recombinant extracellular IL-23R. A collection of 34 IL-23R-binding proteins (called REX binders), corresponding to 18 different sequence variants, was used to identify a group of ligands that inhibited binding of the recombinant p19 subunit of IL-23, or the biologically active human IL-23 cytokine, to the recombinant IL-23R or soluble IL-23R-IgG chimera. The strongest competitors for IL-23R binding in ELISA were confirmed to recognize human IL-23R-IgG in surface plasmon resonance experiments, estimating the binding affinity in the sub- to nanomolar range. We further demonstrated that several REX variants bind to human leukemic cell lines K-562, THP-1 and Jurkat, and this binding correlated with IL-23R cell-surface expression. The REX125, REX009 and REX128 variants competed with the p19 protein for binding to THP-1 cells. Moreover, the presence of REX125, REX009 and REX115 variants significantly inhibited the IL-23-driven expansion of IL-17-producing primary human CD4+ T-cells. Thus, we conclude that unique IL-23R antagonists derived from the ABD scaffold were generated that might be useful in designing novel anti-inflammatory biologicals. Proteins 2014; 82:975–989.
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Affiliation(s)
- Milan Kuchař
- Laboratory of Ligand Engineering, Institute of Biotechnology AS CR, v. v. i., Vídeňská 1083, 142 20 Prague, Czech Republic
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Mikulecký P, Černý J, Biedermannová L, Petroková H, Kuchař M, Vondrášek J, Malý P, Šebo P, Schneider B. Increasing affinity of interferon-γ receptor 1 to interferon-γ by computer-aided design. BIOMED RESEARCH INTERNATIONAL 2013; 2013:752514. [PMID: 24199198 PMCID: PMC3807708 DOI: 10.1155/2013/752514] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/06/2013] [Accepted: 08/13/2013] [Indexed: 12/12/2022]
Abstract
We describe a computer-based protocol to design protein mutations increasing binding affinity between ligand and its receptor. The method was applied to mutate interferon-γ receptor 1 (IFN-γ-Rx) to increase its affinity to natural ligand IFN-γ, protein important for innate immunity. We analyzed all four available crystal structures of the IFN-γ-Rx/IFN-γ complex to identify 40 receptor residues forming the interface with IFN-γ. For these 40 residues, we performed computational mutation analysis by substituting each of the interface receptor residues by the remaining standard amino acids. The corresponding changes of the free energy were calculated by a protocol consisting of FoldX and molecular dynamics calculations. Based on the computed changes of the free energy and on sequence conservation criteria obtained by the analysis of 32 receptor sequences from 19 different species, we selected 14 receptor variants predicted to increase the receptor affinity to IFN-γ. These variants were expressed as recombinant proteins in Escherichia coli, and their affinities to IFN-γ were determined experimentally by surface plasmon resonance (SPR). The SPR measurements showed that the simple computational protocol succeeded in finding two receptor variants with affinity to IFN-γ increased about fivefold compared to the wild-type receptor.
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Affiliation(s)
- Pavel Mikulecký
- Institute of Biotechnology AS CR, v. v. i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Jiří Černý
- Institute of Biotechnology AS CR, v. v. i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Lada Biedermannová
- Institute of Biotechnology AS CR, v. v. i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Hana Petroková
- Institute of Biotechnology AS CR, v. v. i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Milan Kuchař
- Institute of Biotechnology AS CR, v. v. i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Jiří Vondrášek
- Institute of Biotechnology AS CR, v. v. i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Petr Malý
- Institute of Biotechnology AS CR, v. v. i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Peter Šebo
- Institute of Biotechnology AS CR, v. v. i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology AS CR, v. v. i., Vídeňská 1083, 142 20 Prague, Czech Republic
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Moal IH, Torchala M, Bates PA, Fernández-Recio J. The scoring of poses in protein-protein docking: current capabilities and future directions. BMC Bioinformatics 2013; 14:286. [PMID: 24079540 PMCID: PMC3850738 DOI: 10.1186/1471-2105-14-286] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/25/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Protein-protein docking, which aims to predict the structure of a protein-protein complex from its unbound components, remains an unresolved challenge in structural bioinformatics. An important step is the ranking of docked poses using a scoring function, for which many methods have been developed. There is a need to explore the differences and commonalities of these methods with each other, as well as with functions developed in the fields of molecular dynamics and homology modelling. RESULTS We present an evaluation of 115 scoring functions on an unbound docking decoy benchmark covering 118 complexes for which a near-native solution can be found, yielding top 10 success rates of up to 58%. Hierarchical clustering is performed, so as to group together functions which identify near-natives in similar subsets of complexes. Three set theoretic approaches are used to identify pairs of scoring functions capable of correctly scoring different complexes. This shows that functions in different clusters capture different aspects of binding and are likely to work together synergistically. CONCLUSIONS All functions designed specifically for docking perform well, indicating that functions are transferable between sampling methods. We also identify promising methods from the field of homology modelling. Further, differential success rates by docking difficulty and solution quality suggest a need for flexibility-dependent scoring. Investigating pairs of scoring functions, the set theoretic measures identify known scoring strategies as well as a number of novel approaches, indicating promising augmentations of traditional scoring methods. Such augmentation and parameter combination strategies are discussed in the context of the learning-to-rank paradigm.
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Affiliation(s)
- Iain H Moal
- Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Super computing Center, Barcelona 08034, Spain
| | - Mieczyslaw Torchala
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Paul A Bates
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Juan Fernández-Recio
- Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Super computing Center, Barcelona 08034, Spain
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Nilvebrant J, Åstrand M, Löfblom J, Hober S. Development and characterization of small bispecific albumin-binding domains with high affinity for ErbB3. Cell Mol Life Sci 2013; 70:3973-85. [PMID: 23728098 PMCID: PMC11113916 DOI: 10.1007/s00018-013-1370-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 04/17/2013] [Accepted: 05/13/2013] [Indexed: 11/27/2022]
Abstract
Affinity proteins based on small scaffolds are currently emerging as alternatives to antibodies for therapy. Similarly to antibodies, they can be engineered to have high affinity for specific proteins. A potential problem with small proteins and peptides is their short in vivo circulation time, which might limit the therapeutic efficacy. To circumvent this issue, we have engineered bispecificity into an albumin-binding domain (ABD) derived from streptococcal Protein G. The inherent albumin binding was preserved while the opposite side of the molecule was randomized for selection of high-affinity binders. Here we present novel ABD variants with the ability to bind to the epidermal growth factor receptor 3 (ErbB3). Isolated candidates were shown to have an extraordinary thermal stability and affinity for ErbB3 in the nanomolar range. Importantly, they were also shown to retain their affinity to albumin, hence demonstrating that the intended strategy to engineer bispecific single-domain proteins against a tumor-associated receptor was successful. Moreover, competition assays revealed that the new binders could block the natural ligand Neuregulin-1 from binding to ErbB3, indicating a potential anti-proliferative effect. These new binders thus represent promising candidates for further development into ErbB3-signaling inhibitors, where the albumin interaction could result in prolonged in vivo half-life.
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Affiliation(s)
- Johan Nilvebrant
- Division of Protein Technology, KTH Royal Institute of Technology, AlbaNova University Center, 106 91 Stockholm, Sweden
| | - Mikael Åstrand
- Division of Protein Technology, KTH Royal Institute of Technology, AlbaNova University Center, 106 91 Stockholm, Sweden
| | - John Löfblom
- Division of Protein Technology, KTH Royal Institute of Technology, AlbaNova University Center, 106 91 Stockholm, Sweden
| | - Sophia Hober
- Division of Protein Technology, KTH Royal Institute of Technology, AlbaNova University Center, 106 91 Stockholm, Sweden
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Nilvebrant J, Hober S. The albumin-binding domain as a scaffold for protein engineering. Comput Struct Biotechnol J 2013; 6:e201303009. [PMID: 24688717 PMCID: PMC3962080 DOI: 10.5936/csbj.201303009] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/31/2013] [Accepted: 08/07/2013] [Indexed: 11/22/2022] Open
Abstract
The albumin-binding domain is a small, three-helical protein domain found in various surface proteins expressed by gram-positive bacteria. Albumin binding is important in bacterial pathogenesis and several homologous domains have been identified. Such albumin-binding regions have been used for protein purification or immobilization. Moreover, improvement of the pharmacokinetics, through the non-covalent association to albumin, by fusing such domains to therapeutic proteins has been shown to be successful. Domains derived from streptococcal protein G and protein PAB from Finegoldia magna, which share a common origin and therefore represent an interesting evolutionary system, have been thoroughly studied structurally and functionally. Their albumin-binding sites have been mapped and these domains form the basis for a wide range of protein engineering approaches. By substitution-mutagenesis they have been engineered to achieve a broader specificity, an increased stability or an improved binding affinity, respectively. Furthermore, novel binding sites have been incorporated either by replacing the original albumin-binding surface, or by complementing it with a novel interaction interface. Combinatorial protein libraries, where several residues have been randomized simultaneously, have generated a large number of new variants with desired binding characteristics. The albumin-binding domain has also been utilized to explore the relationship between three-dimensional structure and amino acid sequence. Proteins with latent structural information built into their sequence, where a single amino acid substitution shifts the equilibrium in favor of a different fold with a new function, have been designed. Altogether, these examples illustrate the versatility of the albumin-binding domain as a scaffold for protein engineering.
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Affiliation(s)
- Johan Nilvebrant
- Division of Protein Technology, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Sophia Hober
- Division of Protein Technology, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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