1
|
David TI, Pestov NB, Korneenko TV, Barlev NA. Non-Immunoglobulin Synthetic Binding Proteins for Oncology. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1232-1247. [PMID: 37770391 DOI: 10.1134/s0006297923090043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 09/30/2023]
Abstract
Extensive application of technologies like phage display in screening peptide and protein combinatorial libraries has not only facilitated creation of new recombinant antibodies but has also significantly enriched repertoire of the protein binders that have polypeptide scaffolds without homology to immunoglobulins. These innovative synthetic binding protein (SBP) platforms have grown in number and now encompass monobodies/adnectins, DARPins, lipocalins/anticalins, and a variety of miniproteins such as affibodies and knottins, among others. They serve as versatile modules for developing complex affinity tools that hold promise in both diagnostic and therapeutic settings. An optimal scaffold typically has low molecular weight, minimal immunogenicity, and demonstrates resistance against various challenging conditions, including proteolysis - making it potentially suitable for peroral administration. Retaining functionality under reducing intracellular milieu is also advantageous. However, paramount to its functionality is the scaffold's ability to tolerate mutations across numerous positions, allowing for the formation of a sufficiently large target binding region. This is achieved through the library construction, screening, and subsequent expression in an appropriate system. Scaffolds that exhibit high thermodynamic stability are especially coveted by the developers of new SBPs. These are steadily making their way into clinical settings, notably as antagonists of oncoproteins in signaling pathways. This review surveys the diverse landscape of SBPs, placing particular emphasis on the inhibitors targeting the oncoprotein KRAS, and highlights groundbreaking opportunities for SBPs in oncology.
Collapse
Affiliation(s)
- Temitope I David
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Laboratory of Molecular Oncology, Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nikolay B Pestov
- Institute of Biomedical Chemistry, Moscow, 119121, Russia.
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Tatyana V Korneenko
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Nikolai A Barlev
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Institute of Cytology Russian Academy of Sciences, St.-Petersburg, 194064, Russia
- School of Medicine, Nazarbayev University, Astana, 010000, Kazakhstan
| |
Collapse
|
2
|
Raeeszadeh-Sarmazdeh M, Boder ET. Yeast Surface Display: New Opportunities for a Time-Tested Protein Engineering System. Methods Mol Biol 2022; 2491:3-25. [PMID: 35482182 DOI: 10.1007/978-1-0716-2285-8_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Yeast surface display has proven to be a powerful tool for the discovery of antibodies and other novel binding proteins and for engineering the affinity and selectivity of existing proteins for their targets. In the decades since the first demonstrations of the approach, the range of yeast display applications has greatly expanded to include many different protein targets and has grown to encompass methods for rapid protein characterization. Here, we briefly summarize the development of yeast display methodologies and highlight several selected examples of recent applications to timely and challenging protein engineering and characterization problems.
Collapse
Affiliation(s)
| | - Eric T Boder
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Zohorsky K, Mequanint K. Designing Biomaterials to Modulate Notch Signaling in Tissue Engineering and Regenerative Medicine. TISSUE ENGINEERING PART B-REVIEWS 2020; 27:383-410. [PMID: 33040694 DOI: 10.1089/ten.teb.2020.0182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The design of cell-instructive biomaterials for tissue engineering and regenerative medicine is at a crossroads. Although the conventional tissue engineering approach is top-down (cells seeded to macroporous scaffolds and mature to form tissues), bottom-up tissue engineering strategies are becoming appealing. With such developments, we can study cell signaling events, thus enabling functional tissue assembly in physiologic and diseased models. Among many important signaling pathways, the Notch signaling pathway is the most diverse in its influence during tissue morphogenesis and repair following injury. Although Notch signaling is extensively studied in developmental biology and cancer biology, our knowledge of designing biomaterial-based Notch signaling platforms and incorporating Notch signaling components into engineered tissue systems is limited. By incorporating Notch signaling to tissue engineering scaffolds, we can direct cell-specific responses and improve engineered tissue maturation. This review will discuss recent progress in the development of Notch signaling biomaterials as a promising target to control cellular fate decisions, including the influences of ligand identity, biophysical material cues, ligand presentation strategies, and mechanotransduction. Notch signaling is consequently of interest to direct, control, and reprogram cellular behavior on a biomaterial surface. We anticipate that discussions in this article will allow for enhanced knowledge and insight into designing Notch targeted biomaterials for various tissue engineering and cell fate determinations. Impact statement Notch signaling is recognized as an important pathway in tissue engineering and regenerative medicine; however, there is no systematic review on this topic. The comprehensive review and perspectives presented here provide an in-depth discussion on ligand presentation strategies both in 2D and in 3D cell culture environments involving biomaterials/scaffolds. In addition, this review article provides insight into the challenges in designing cell surrogate biomaterials capable of providing Notch signals. To the best of the authors' knowledge, this is the first review relevant to the fields of tissue engineering.
Collapse
Affiliation(s)
- Kathleen Zohorsky
- School of Biomedical Engineering and The University of Western Ontario, London, Canada
| | - Kibret Mequanint
- School of Biomedical Engineering and The University of Western Ontario, London, Canada.,Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, Canada
| |
Collapse
|
5
|
Mukherjee A, Singh R, Udayan S, Biswas S, Reddy PP, Manmadhan S, George G, Kumar S, Das R, Rao BM, Gulyani A. A Fyn biosensor reveals pulsatile, spatially localized kinase activity and signaling crosstalk in live mammalian cells. eLife 2020; 9:50571. [PMID: 32017701 PMCID: PMC7000222 DOI: 10.7554/elife.50571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
Cell behavior is controlled through spatio-temporally localized protein activity. Despite unique and often contradictory roles played by Src-family-kinases (SFKs) in regulating cell physiology, activity patterns of individual SFKs have remained elusive. Here, we report a biosensor for specifically visualizing active conformation of SFK-Fyn in live cells. We deployed combinatorial library screening to isolate a binding-protein (F29) targeting activated Fyn. Nuclear-magnetic-resonance (NMR) analysis provides the structural basis of F29 specificity for Fyn over homologous SFKs. Using F29, we engineered a sensitive, minimally-perturbing fluorescence-resonance-energy-transfer (FRET) biosensor (FynSensor) that reveals cellular Fyn activity to be spatially localized, pulsatile and sensitive to adhesion/integrin signaling. Strikingly, growth factor stimulation further enhanced Fyn activity in pre-activated intracellular zones. However, inhibition of focal-adhesion-kinase activity not only attenuates Fyn activity, but abolishes growth-factor modulation. FynSensor imaging uncovers spatially organized, sensitized signaling clusters, direct crosstalk between integrin and growth-factor-signaling, and clarifies how compartmentalized Src-kinase activity may drive cell fate.
Collapse
Affiliation(s)
- Ananya Mukherjee
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,SASTRA University, Thanjavur, India
| | - Randhir Singh
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Sreeram Udayan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Sayan Biswas
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | | | - Saumya Manmadhan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Geen George
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Shilpa Kumar
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Ranabir Das
- National Centre for Biological Sciences, Bangalore, India
| | - Balaji M Rao
- North Carolina State University, Raleigh, United States
| | - Akash Gulyani
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| |
Collapse
|
6
|
Gebauer M, Skerra A. Engineering of binding functions into proteins. Curr Opin Biotechnol 2019; 60:230-241. [DOI: 10.1016/j.copbio.2019.05.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/07/2019] [Indexed: 12/13/2022]
|
7
|
Abstract
The critical need for renewable, high-quality affinity reagents in biological research, as well as for diagnostic and therapeutic applications, has required the development of new platforms of discovery. Yeast display is one of the main methods of in vitro display technology with phage display. Yeast display has been chosen by numerous groups to refine both affinity and specificity of antibodies because it enables fine discrimination between mutant clones of similar affinity. In addition, the construction of display libraries of antibody fragments in yeast permits to sample the immune antibody repertoire more fully than using phage. This chapter gives an updated overview of the available systems of yeast display platforms and libraries, followed up by technical descriptions of selection methods of antibody fragments by yeast display.
Collapse
|