Chemoproteomic Capture Reagents With Solid-Phase DADPS Synthesis

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Solution Overview

Problem

Existing synthetic strategies for incorporating dialkoxydiphenylsilane (DADPS) moieties into chemoproteomics capture reagents are limited, leading to low yields and inefficiencies, particularly for isotopically labeled reagents, and do not support compatibility with all sequence-specific proteases.

Innovation Solution

A high-yielding solid-phase synthesis method using versatile fluorenylmethyl carbamate (Fmoc) functionalized DADPS building blocks, such as NBIV-044 and NBIV-053, is developed, enabling the synthesis of isotopically labeled reagents with a stable ether linkage and compatibility with various proteases.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Productivity

If traditional synthetic strategies are used to incorporate DADPS moieties into chemoproteomics capture reagents, then the reagents can be produced, but the synthesis yields are low and the process is inefficient

Engineering Contradiction:

Improvesynthesis yieldVSAvoidsynthetic complexity

Core Design Contradiction:

ProductivityVSEase of manufacture

Solution Approach 1:

The synthesis is divided into modular stages using solid-phase peptide synthesis (SPPS), where the DADPS moiety is incorporated as a separate building block (e.g., Fmoc-Dadps-OH) during stepwise amino acid assembly. This segmentation allows for standardized, high-yielding coupling reactions at each stage, avoiding the low yields associated with traditional solution-phase methods that require multiple purification steps.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

A solid support (resin) acts as an intermediary carrier throughout the synthesis process. The growing peptide chain with DADPS moiety remains attached to the solid support during washing and coupling steps, enabling efficient separation of reactants from products without requiring intermediate purification. This eliminates material loss and improves overall synthesis yield.

Inventive Principle:

Principle #24Intermediary (Mediator)

2Adaptability or versatility

If traditional synthesis methods are used, then reagents can be produced, but isotopically labeled reagents cannot be efficiently synthesized

Engineering Contradiction:

Improveisotopic labeling capabilityVSAvoidsynthesis efficiency

Core Design Contradiction:

Adaptability or versatilityVSProductivity

Solution Approach 1:

The SPPS methodology provides a universal platform that works for both standard and isotopically labeled amino acids. Isotopically labeled building blocks (e.g., 13C6-L-arginine, 15N-L-lysine) can be directly incorporated into the peptide sequence at any position during the standard coupling cycle, enabling efficient synthesis of isotopically labeled chemoproteomics reagents without requiring separate synthetic pathways.

Inventive Principle:

Principle #6Universality (Multi-functionality)

3Adaptability or versatility

If existing synthetic strategies are used, then capture reagents can be made, but compatibility with all sequence-specific proteases is not achieved

Engineering Contradiction:

Improveprotease compatibilityVSAvoidreagent structure complexity

Core Design Contradiction:

Adaptability or versatilityVSDevice complexity

Solution Approach 1:

The DADPS moiety is strategically positioned at specific locations within the capture reagent structure (e.g., at N- or C-termini, or at specific amino acid positions within the peptide sequence) rather than being uniformly distributed. This localized placement ensures that the cleavable DADPS group does not interfere with protease active sites, enabling compatibility with multiple sequence-specific proteases while maintaining the desired cleavage functionality at the designated location.

Inventive Principle:

Principle #3Local quality

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

The method allows for the rapid and high-yielding synthesis of chemoproteomic capture reagents, enhancing peptide and protein coverage, and identifying cysteine-containing peptides, with applications in chemoproteomics analysis and covalent ligand discovery.

Implementation Method 1

cleaving the support-enrichment handle-solid-phase compatible cleavable linker-isopically labelled amino acid conjugate from the solid support, thereby synthesizing the chemoproteomic capture reagent

Methodology Applied

Scientific EffectChemical Bonding: Chemical Bonding