1
|
Li X, Kulakova L, Jones K, Toth EA, Mitchell MK, Mendez Q, Weiner MP, Fuerst TR. Site-directed neutralizing antibodies targeting structural sites on SARS-CoV-2 spike protein. N Biotechnol 2024; 80:27-36. [PMID: 38128698 PMCID: PMC10954356 DOI: 10.1016/j.nbt.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/20/2023] [Accepted: 12/17/2023] [Indexed: 12/23/2023]
Abstract
'Epivolve' (epitope evolution) is an innovative paratope-evolving technology using a haptenated peptide or protein immunogen as a means of directing the in vivo immune response to specifically targeted sites at a one amino acid residue resolution. Guided by protein structural analysis, Epivolve technology was tested to develop site-directed neutralizing antibodies (nAbs) in a systematic fashion against the SARS-CoV-2 Receptor Binding Domain (RBD). Thirteen solvent-exposed sites covering the ACE2 receptor-binding interface were targeted. Immunogens composed of each targeted site were used to immunize rabbits in separate cohorts. In vivo site-directed immune responses against all 13 targets were demonstrated by B cell secreted IgG and recombinant IgG testing. One site, SL13 (Y505) which mutates from tyrosine to histidine in the SARS-CoV-2 Omicron variant, was chosen as a proof-of-concept (PoC) model for further functional monoclonal antibody development. Epivolve technology demonstrated the capabilities of generating pan-variant antibodies and nAbs against the SARS-CoV-2 primary strain and the Omicron variant.
Collapse
Affiliation(s)
- Xiaofeng Li
- Abbratech Inc., 25 Business Park Drive, Suite C, Branford, CT 06405, USA.
| | - Liudmila Kulakova
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Kezzia Jones
- Abbratech Inc., 25 Business Park Drive, Suite C, Branford, CT 06405, USA
| | - Eric A Toth
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | | | - Qiana Mendez
- Abbratech Inc., 25 Business Park Drive, Suite C, Branford, CT 06405, USA
| | - Michael P Weiner
- Abbratech Inc., 25 Business Park Drive, Suite C, Branford, CT 06405, USA
| | - Thomas R Fuerst
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| |
Collapse
|
2
|
Coorssen JR, Padula MP. Proteomics-The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience. Proteomes 2024; 12:14. [PMID: 38651373 PMCID: PMC11036260 DOI: 10.3390/proteomes12020014] [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: 03/17/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
With growing recognition and acknowledgement of the genuine complexity of proteomes, we are finally entering the post-proteogenomic era. Routine assessment of proteomes as inferred correlates of gene sequences (i.e., canonical 'proteins') cannot provide the necessary critical analysis of systems-level biology that is needed to understand underlying molecular mechanisms and pathways or identify the most selective biomarkers and therapeutic targets. These critical requirements demand the analysis of proteomes at the level of proteoforms/protein species, the actual active molecular players. Currently, only highly refined integrated or integrative top-down proteomics (iTDP) enables the analytical depth necessary to provide routine, comprehensive, and quantitative proteome assessments across the widest range of proteoforms inherent to native systems. Here we provide a broad perspective of the field, taking in historical and current realities, to establish a more balanced understanding of where the field has come from (in particular during the ten years since Proteomes was launched), current issues, and how things likely need to proceed if necessary deep proteome analyses are to succeed. We base this in our firm belief that the best proteomic analyses reflect, as closely as possible, the native sample at the moment of sampling. We also seek to emphasise that this and future analytical approaches are likely best based on the broad recognition and exploitation of the complementarity of currently successful approaches. This also emphasises the need to continuously evaluate and further optimize established approaches, to avoid complacency in thinking and expectations but also to promote the critical and careful development and introduction of new approaches, most notably those that address proteoforms. Above all, we wish to emphasise that a rigorous focus on analytical quality must override current thinking that largely values analytical speed; the latter would certainly be nice, if only proteoforms could thus be effectively, routinely, and quantitatively assessed. Alas, proteomes are composed of proteoforms, not molecular species that can be amplified or that directly mirror genes (i.e., 'canonical'). The problem is hard, and we must accept and address it as such, but the payoff in playing this longer game of rigorous deep proteome analyses is the promise of far more selective biomarkers, drug targets, and truly personalised or even individualised medicine.
Collapse
Affiliation(s)
- Jens R. Coorssen
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
- Institute for Globally Distributed Open Research and Education (IGDORE), St. Catharines, ON L2N 4X2, Canada
| | - Matthew P. Padula
- School of Life Sciences and Proteomics, Lipidomics and Metabolomics Core Facility, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| |
Collapse
|
3
|
Thota SS, Allen GL, Grahn AK, Kay BK. Engineered FHA domains can bind to a variety of Phosphothreonine-containing peptides. Protein Eng Des Sel 2024; 37:gzae014. [PMID: 39276365 PMCID: PMC11436287 DOI: 10.1093/protein/gzae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 08/30/2024] [Accepted: 09/12/2024] [Indexed: 09/17/2024] Open
Abstract
Antibodies play a crucial role in monitoring post-translational modifications, like phosphorylation, which regulates protein activity and location; however, commercial polyclonal and monoclonal antibodies have limitations in renewability and engineering compared to recombinant affinity reagents. A scaffold based on the Forkhead-associated domain (FHA) has potential as a selective affinity reagent for this post-translational modification. Engineered FHA domains, termed phosphothreonine-binding domains (pTBDs), with limited cross-reactivity were isolated from an M13 bacteriophage display library by affinity selection with phosphopeptides corresponding to human mTOR, Chk2, 53BP1, and Akt1 proteins. To determine the specificity of the representative pTBDs, we focused on binders to the pT543 phosphopeptide (536-IDEDGENpTQIEDTEP-551) of the DNA repair protein 53BP1. ELISA and western blot experiments have demonstrated the pTBDs are specific to phosphothreonine, demonstrating the potential utility of pTBDs for monitoring the phosphorylation of specific threonine residues in clinically relevant human proteins.
Collapse
Affiliation(s)
- Srinivas S Thota
- Tango Biosciences, 2201 W. Campbell Park Drive, Chicago, IL 60612-4092 USA
| | - Grace L Allen
- Tango Biosciences, 2201 W. Campbell Park Drive, Chicago, IL 60612-4092 USA
| | - Ashley K Grahn
- Tango Biosciences, 2201 W. Campbell Park Drive, Chicago, IL 60612-4092 USA
| | - Brian K Kay
- Tango Biosciences, 2201 W. Campbell Park Drive, Chicago, IL 60612-4092 USA
| |
Collapse
|
4
|
Mendez Q, Driscoll HA, Mirando GR, Acca F, Chapados CD, Jones KS, Weiner M, Li X, Ferguson MR. MILKSHAKE Western blot and Sundae ELISA: We all scream for better antibody validation. J Immunol Methods 2023; 521:113540. [PMID: 37597727 PMCID: PMC10568614 DOI: 10.1016/j.jim.2023.113540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Knowing that an antibody's sensitivity and specificity is accurate is crucial for reliable data collection. This certainty is especially difficult to achieve for antibodies (Abs) which bind post-translationally modified proteins. Here we describe two validation methods using surrogate proteins in western blot and ELISA. The first method, which we termed "MILKSHAKE" is a modified maltose binding protein, hence the name, that is enzymatically conjugated to a peptide from the chosen target which is either modified or non-modified at the residue of interest. The surety of the residue's modification status can be used to confirm Ab specificity to the target's post-translational modification (PTM). The second method uses a set of surrogate proteins, which we termed "Sundae". Sundae consists of a set of modified maltose binding proteins with a genetically encoded target sequence, each of which contains a single amino acid substitution at one position of interest. With Sundae, Abs can be evaluated for binding specificities to all twenty amino acids at a single position. Combining MILKSHAKE and Sundae methods, Ab specificity can be determined at a single-residue resolution. These data improve evaluation of commercially available Abs and identify off-target effects for Research-Use-Only and therapeutic Abs.
Collapse
Affiliation(s)
- Qiana Mendez
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Holland A Driscoll
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Gregory R Mirando
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Felicity Acca
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Cassandra D Chapados
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Kezzia S Jones
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Michael Weiner
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Xiaofeng Li
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Mary R Ferguson
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| |
Collapse
|
5
|
Ferguson MR, Mendez QM, Acca FE, Chapados CD, Driscoll HA, Jones KS, Mirando G, Weiner MP, Li X. Validation and the Determination of Antibody Bioactivity Using MILKSHAKE and Sundae Protocols. Methods Mol Biol 2023; 2702:451-465. [PMID: 37679635 PMCID: PMC10568615 DOI: 10.1007/978-1-0716-3381-6_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
To develop reproducible results, it is critical that all reagents used in an experiment be validated in an alternative or independent method. We present two such independent methods for determining the specificity of antibodies: (1) "MILKSHAKE," which can be used to validate the liability and specificity of antibodies directed against post-translationally-modified epitopes, and (2) "Sundae," which is a more complete alanine-like scanning method that can be used to better understand the binding and bioactivity of specific residues of a protein. We apply both of these methods to the interaction between an antibody and its antigen.
Collapse
|
6
|
Li X, Jones KS, Acca FE, Chapados CD, Driscoll HA, Fuller EP, Mendez QM, Mirando G, Weiner MP, Ferguson MR. Epivolve: A Protocol for Site-Directed Antibodies. Methods Mol Biol 2023; 2702:587-601. [PMID: 37679640 PMCID: PMC10568616 DOI: 10.1007/978-1-0716-3381-6_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Researchers can often successfully generate antibodies to predicted epitopes. Especially when the epitopes are on the surface of a protein or in a hydrophilic loop. But it is difficult to direct recombinant antibodies to bind either to- or near a specific amino acid on a protein or peptide. We have developed a unique immune-targeting strategy, that we call "Epivolve," that enables us to make site-specific antibodies (Abs). Epivolve technology leverages a highly immunogenic modified amino acid that acts as a "pseudo-hapten" immuno-target and takes advantage of Ab affinity maturation technologies to make high-affinity site-specific antibodies. Epivolve functions by the evolution of an Ab paratope to either synonymous or especially non-synonymous amino acid (aa) binding. Here we describe the use of Epivolve technology in phage display and the protocols for developing site-specific antibodies.
Collapse
Affiliation(s)
| | | | | | | | | | - Emily P Fuller
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | | | | | | | | |
Collapse
|