Cell-Based Screening for Native Antigen Epitopes
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Solution Overview
Problem
Traditional methods for screening binding polypeptides, such as antibodies, fail to recognize cell-surface antigens in their native conformation when solubilized from the plasma membrane, leading to ineffective identification of therapeutically useful antibodies that can bind specifically to native forms of cell-surface antigens.
Innovation Solution
The method involves contacting a variegated nucleic acid-display library of binding polypeptides with cell-surface antigens displayed on cells and isolating library members that specifically bind to these antigens, using techniques like DNA display and deep sequencing to identify high-affinity binders that recognize native cell-surface antigens.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If soluble antigens are used for screening binding polypeptides, then the screening process is simple and efficient, but the conformational epitopes are altered and binding polypeptides cannot recognize native antigens
Solution Approach 1:
The patent uses cell surfaces as natural copies of the native antigen environment, preserving the three-dimensional conformational epitopes that are lost when antigens are solubilized. By screening against intact cells rather than soluble antigens, the method maintains the native structure of cell-surface antigens while enabling efficient identification of binding polypeptides with therapeutic relevance.
2Ease of operation
If cell-surface antigens are solubilized from the plasma membrane, then the antigens become accessible for traditional screening methods, but the conformational epitopes are altered resulting in failure to generate binding polypeptides
Solution Approach 1:
The patent introduces whole cells as an intermediary system that presents cell-surface antigens in their native conformational state. This intermediary approach allows binding polypeptides to be screened against the correct three-dimensional structure of epitopes, bridging the gap between antigen accessibility and structural integrity without requiring solubilization.
3Ease of manufacture
If traditional soluble antigen screening is used, then the method is well-established and straightforward, but it fails to identify binding polypeptides that recognize native cell-surface antigens
Solution Approach 1:
The patent transitions from static soluble antigen screening to dynamic cell-based screening, where antigens are presented in their native, functional environment on living or fixed cells. This dynamic approach preserves the physiological conformation of cell-surface antigens and enables identification of binding polypeptides with true therapeutic potential, while the standardized cell-based protocol maintains operational simplicity.
Data Source
AI summary
The invention provides methods and compositions for identifying binding polypeptides (e.g., antibodies or antigen binding fragments thereof) that specifically binds to a cell-surface antigen. The methods of the invention generally comprise contacting a variegated nucleic acid-display library of binding polypeptides with a cell-surface antigen displayed on the exterior surface of a cell; and isolating from the library at least one library member that specifically binds to the cell-surface antigen on the exterior surface of the cell.