Low-cost synthesis of peptide libraries and their use for binding studies via temperature-related intensity change

Molecular dissection of an immunodominant epitope in Kv1.2-exclusive autoimmunity

Introduction

Subgroups of autoantibodies directed against voltage-gated potassium channel (Kv) complex components have been associated with immunotherapy-responsive clinical syndromes. The high prevalence and the role of autoantibodies directly binding Kv remain, however, controversial. Our objective was to determine Kv autoantibody binding requirements and to clarify their contribution to the observed immune response.

Methods

Binding epitopes were studied in sera (n = 36) and cerebrospinal fluid (CSF) (n = 12) from a patient cohort positive for Kv1.2 but negative for 32 common neurological autoantigens and controls (sera n = 18 and CSF n = 5) by phospho and deep mutational scans. Autoantibody specificity and contribution to the observed immune response were resolved on recombinant cells, cerebellum slices, and nerve fibers.

Results

83% of the patients (30/36) within the studied cohort shared one out of the two major binding epitopes with Kv1.2-3 reactivity. Eleven percent (4/36) of the serum samples showed no binding. Fingerprinting resolved close to identical sequence requirements for both shared epitopes. Kv autoantibody response is directed against juxtaparanodal regions in peripheral nerves and the axon initial segment in central nervous system neurons and exclusively mediated by the shared epitopes.

Discussion

Systematic mapping revealed two shared autoimmune responses, with one dominant Kv1.2-3 autoantibody epitope being unexpectedly prevalent. The conservation of the molecular binding requirements among these patients indicates a uniform autoantibody repertoire with monospecific reactivity. The enhanced sensitivity of the epitope-based (10/12) compared with that of the cell-based detection (7/12) highlights its use for detection. The determined immunodominant epitope is also the primary immune response visible in tissue, suggesting a diagnostic significance and a specific value for routine screening.

Solid-phase peptide synthesis in 384-well plates

Newer solid-phase peptide synthesis and release strategies enable the production of short peptides with high purity, allowing direct screening for desired bioactivity without prior chromatographic purification. However, the maximum number of peptides that can currently be synthesized per microplate reactor is 96, allowing the parallel synthesis of 384 peptides in modern devices that have space for 4 microplate reactors. To synthesize larger numbers of peptides, we modified a commercially available peptide synthesizer to enable the production of peptides in 384-well plates, which allows the synthesis of 1,536 peptides in one run (4 × 384 peptides). We report new hardware components and customized software that allowed for the synthesis of 1,536 short peptides in good quantity (average > 0.5 μmol), at high concentration (average > 10 mM), and decent purity without purification (average > 80%). The high-throughput peptide synthesis, which we developed with peptide drug development in mind, may be widely used for peptide library synthesis and screening, antibody epitope scanning, epitope mimetic development, or protease/kinase substrate screening.

Human antibody profiling technologies for autoimmune disease

Autoimmune diseases are caused by the break-down in self-tolerance mechanisms and can result in the generation of autoantibodies specific to human antigens. Human autoantigen profiling technologies such as solid surface arrays and display technologies are powerful high-throughput technologies utilised to discover and map novel autoantigens associated with disease. This review compares human autoantigen profiling technologies including the application of these approaches in chronic and post-infectious autoimmune disease. Each technology has advantages and limitations that should be considered when designing new projects to profile autoantibodies. Recent studies that have utilised these technologies across a range of diseases have highlighted marked heterogeneity in autoantibody specificity between individuals as a frequent feature. This individual heterogeneity suggests that epitope spreading maybe an important mechanism in the pathogenesis of autoimmune disease in general and likely contributes to inflammatory tissue damage and symptoms. Studies focused on identifying autoantibody biomarkers for diagnosis should use targeted data analysis to identify the rarer public epitopes and antigens, common between individuals. Thus, utilisation of human autoantigen profiling technology, combined with different analysis approaches, can illuminate both pathogenesis and biomarker discovery.

Peptide Microarray-Based Protein Interaction Studies Across Affinity Ranges: Enzyme Stalling, Cross-Linking, Depletion, and Neutralization

While an ever-increasing number of protein-protein interactions were studied by peptide microarrays with great success, array-based investigations of transiently binding proteins, such as HDACs, and precise binding quantification, remained challenging. Here, we present an updated protocol for the preparation and use of peptide microarrays including the necessary adjustments for simple semi-quantitative and precise measurements across affinity ranges. This procedure describes the mass spectrometric controlled preparation of peptide microarrays in μSPOT format, and their application in binding profiling of recombinant, as well as endogenous, native proteins. We further highlight how cross-linking, blocking, and enzyme stalling can be leveraged to enhance sensitivity and describe how in situ on-chip binding neutralization can enhance the predictive value and robustness of the binding readout. Finally, we included examples for the integration of precise biophysical binding readouts that complement the traditional array-based binding assays.

Multivalent binding kinetics resolved by fluorescence proximity sensing

Multivalent protein interactors are an attractive modality for probing protein function and exploring novel pharmaceutical strategies. The throughput and precision of state-of-the-art methodologies and workflows for the effective development of multivalent binders is currently limited by surface immobilization, fluorescent labelling and sample consumption. Using the gephyrin protein, the master regulator of the inhibitory synapse, as benchmark, we exemplify the application of Fluorescence proximity sensing (FPS) for the systematic kinetic and thermodynamic optimization of multivalent peptide architectures. High throughput synthesis of +100 peptides with varying combinatorial dimeric, tetrameric, and octameric architectures combined with direct FPS measurements resolved on-rates, off-rates, and dissociation constants with high accuracy and low sample consumption compared to three complementary technologies. The dataset and its machine learning-based analysis deciphered the relationship of specific architectural features and binding kinetics and thereby identified binders with unprecedented protein inhibition capacity; thus, highlighting the value of FPS for the rational engineering of multivalent inhibitors.

Fluorescence proximity sensing enables high throughput determination of binding affinities and kinetics of peptide inhibitors with varying valency and multivalent architecture.