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Li R, Wilderotter S, Stoddard M, Van Egeren D, Chakravarty A, Joseph-McCarthy D. Computational identification of antibody-binding epitopes from mimotope datasets. FRONTIERS IN BIOINFORMATICS 2024; 4:1295972. [PMID: 38463209 PMCID: PMC10920257 DOI: 10.3389/fbinf.2024.1295972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 01/24/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction: A fundamental challenge in computational vaccinology is that most B-cell epitopes are conformational and therefore hard to predict from sequence alone. Another significant challenge is that a great deal of the amino acid sequence of a viral surface protein might not in fact be antigenic. Thus, identifying the regions of a protein that are most promising for vaccine design based on the degree of surface exposure may not lead to a clinically relevant immune response. Methods: Linear peptides selected by phage display experiments that have high affinity to the monoclonal antibody of interest ("mimotopes") usually have similar physicochemical properties to the antigen epitope corresponding to that antibody. The sequences of these linear peptides can be used to find possible epitopes on the surface of the antigen structure or a homology model of the antigen in the absence of an antigen-antibody complex structure. Results and Discussion: Herein we describe two novel methods for mapping mimotopes to epitopes. The first is a novel algorithm named MimoTree that allows for gaps in the mimotopes and epitopes on the antigen. More specifically, a mimotope may have a gap that does not match to the epitope to allow it to adopt a conformation relevant for binding to an antibody, and residues may similarly be discontinuous in conformational epitopes. MimoTree is a fully automated epitope detection algorithm suitable for the identification of conformational as well as linear epitopes. The second is an ensemble approach, which combines the prediction results from MimoTree and two existing methods.
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Affiliation(s)
- Rang Li
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | - Sabrina Wilderotter
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | | | - Debra Van Egeren
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, United States
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Sunderland KS, Yang M, Mao C. Phage-Enabled Nanomedicine: From Probes to Therapeutics in Precision Medicine. Angew Chem Int Ed Engl 2017; 56:1964-1992. [PMID: 27491926 PMCID: PMC5311110 DOI: 10.1002/anie.201606181] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Indexed: 01/08/2023]
Abstract
Both lytic and temperate bacteriophages (phages) can be applied in nanomedicine, in particular, as nanoprobes for precise disease diagnosis and nanotherapeutics for targeted disease treatment. Since phages are bacteria-specific viruses, they do not naturally infect eukaryotic cells and are not toxic to them. They can be genetically engineered to target nanoparticles, cells, tissues, and organs, and can also be modified with functional abiotic nanomaterials for disease diagnosis and treatment. This Review will summarize the current use of phage structures in many aspects of precision nanomedicine, including ultrasensitive biomarker detection, enhanced bioimaging for disease diagnosis, targeted drug and gene delivery, directed stem cell differentiation, accelerated tissue formation, effective vaccination, and nanotherapeutics for targeted disease treatment. We will also propose future directions in the area of phage-based nanomedicines, and discuss the state of phage-based clinical trials.
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Affiliation(s)
- Kegan S Sunderland
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma, 73019, USA
| | - Mingying Yang
- Institute of Applied Bioresource Research, College of Animal Science, Zhejiang University, Yuhangtang Road 866, Hangzhou, Zhejiang, 310058, China
| | - Chuanbin Mao
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma, 73019, USA
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
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Sunderland KS, Yang M, Mao C. Nanomedizin auf Phagenbasis: von Sonden zu Therapeutika für eine Präzisionsmedizin. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201606181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Kegan S. Sunderland
- Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center University of Oklahoma 101 Stephenson Parkway Norman Oklahoma 73019 USA
| | - Mingying Yang
- Institute of Applied Bioresource Research College of Animal Science Zhejiang University Yuhangtang Road 866 Hangzhou Zhejiang 310058 China
| | - Chuanbin Mao
- Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center University of Oklahoma 101 Stephenson Parkway Norman Oklahoma 73019 USA
- School of Materials Science and Engineering Zhejiang University Hangzhou Zhejiang 310027 China
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Aghebati-Maleki L, Bakhshinejad B, Baradaran B, Motallebnezhad M, Aghebati-Maleki A, Nickho H, Yousefi M, Majidi J. Phage display as a promising approach for vaccine development. J Biomed Sci 2016; 23:66. [PMID: 27680328 PMCID: PMC5041315 DOI: 10.1186/s12929-016-0285-9] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/13/2016] [Indexed: 12/31/2022] Open
Abstract
Bacteriophages are specific antagonists to bacterial hosts. These viral entities have attracted growing interest as optimal vaccine delivery vehicles. Phages are well-matched for vaccine design due to being highly stable under harsh environmental conditions, simple and inexpensive large scale production, and potent adjuvant capacities. Phage vaccines have efficient immunostimulatory effects and present a high safety profile because these viruses have made a constant relationship with the mammalian body during a long-standing evolutionary period. The birth of phage display technology has been a turning point in the development of phage-based vaccines. Phage display vaccines are made by expressing multiple copies of an antigen on the surface of immunogenic phage particles, thereby eliciting a powerful and effective immune response. Also, the ability to produce combinatorial peptide libraries with a highly diverse pool of randomized ligands has transformed phage display into a straightforward, versatile and high throughput screening methodology for the identification of potential vaccine candidates against different diseases in particular microbial infections. These libraries can be conveniently screened through an affinity selection-based strategy called biopanning against a wide variety of targets for the selection of mimotopes with high antigenicity and immunogenicity. Also, they can be panned against the antiserum of convalescent individuals to recognize novel peptidomimetics of pathogen-related epitopes. Phage display has represented enormous promise for finding new strategies of vaccine discovery and production and current breakthroughs promise a brilliant future for the development of different phage-based vaccine platforms.
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Affiliation(s)
- Leili Aghebati-Maleki
- Immunology Research Center, Tabriz University of Medical sciences, Tabriz, Iran.,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Babak Bakhshinejad
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Ali Aghebati-Maleki
- Immunology Research Center, Tabriz University of Medical sciences, Tabriz, Iran
| | - Hamid Nickho
- Immunology Research Center, Tabriz University of Medical sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Jafar Majidi
- Immunology Research Center, Tabriz University of Medical sciences, Tabriz, Iran. .,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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