Clickable Photo-Affinity Probes for NAD+ Binding Protein Screening

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Solution Overview

Problem

There is a lack of broadly useful chemical tools for profiling and discovering NAD-binding proteins, given the recent discoveries of non-canonical NAD binding proteins suggesting a larger NAD interactome than previously thought.

Innovation Solution

Development of clickable, photo-affinity labeling (PAL) probes, 2-ad-BAD and 6-ad-BAD, designed to label NAD+ consumers such as PARP-1 and PARP-10, allowing for UV-dependent covalent labeling and profiling of NAD-binding proteins, including adenylate kinase 1, through chemical proteomics.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Adaptability or versatility

If conventional chemical tools are used for profiling NAD-binding proteins, then existing methodologies can be applied, but the discovery of non-canonical NAD binding proteins indicates that the current tools are insufficient and cannot capture the full NAD interactome

Engineering Contradiction:

Improvecapability to profile NAD-binding proteinsVSAvoidaccuracy in identifying NAD interactome

Core Design Contradiction:

Adaptability or versatilityVSReliability

Solution Approach 1:

The patent modifies the chemical structure of NAD+ analogs by introducing photo-reactive groups at specific positions (2-ad-BAD and 6-ad-BAD), changing the chemical parameters to enable covalent bonding with NAD-binding proteins while maintaining NAD+ binding affinity, thus improving the reliability of interactome profiling

Inventive Principle:

Principle #35Parameter changes

Solution Approach 2:

The patent uses photo-reactive NAD+ analogs as intermediary molecules that first bind to NAD-binding proteins through NAD+ interaction, then undergo photo-crosslinking to form covalent bonds, serving as a mediator to capture the NAD interactome with high reliability

Inventive Principle:

Principle #24Intermediary (Mediator)

2Measurement precision

If photo-affinity labeling probes are designed to label NAD+ consumers, then specific proteins like PARP-1 and PARP-10 can be targeted, but the labeling may be influenced by contextual factors such as DNA binding status

Engineering Contradiction:

Improvespecificity of PARP labelingVSAvoidcomplexity of interpreting labeling results

Core Design Contradiction:

Measurement precisionVSEase of operation

Solution Approach 1:

The patent introduces photo-reactive groups at specific local positions (2-position or 6-position) of the NAD+ analog structure, creating position-specific probes (2-ad-BAD for PARP-1, 6-ad-BAD for PARP-10) that provide localized labeling specificity while maintaining overall NAD+ binding function

Inventive Principle:

Principle #3Local quality

Solution Approach 2:

Instead of using the natural NAD+ substrate to label proteins, the patent inverts the approach by using NAD+ analogs with built-in photo-reactive groups that can be activated by UV light to form covalent bonds, reversing the conventional substrate-product relationship to achieve controllable labeling

Inventive Principle:

Principle #13The other way round (Inversion)

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 probes effectively label known and unknown NAD-binding proteins, enabling profiling of the NAD interactome and assessing PARP inhibitor selectivity across PARP family members, with 2-ad-BAD showing context-dependent labeling of PARP-1 and PARP-10.

Implementation Method 1

clickable, photo-affinity labeling (PAL) probes, 2- and 6-ad-BAD, for interrogating the NAD interactome. We show that 2-ad-BAD can label the NAD+-consumers PARP-1 and PARP-10 in a UV-dependent manner

Methodology Applied

Scientific EffectPhoto-affinity labeling: Photopolymerisation

Implementation Method 2

2-ad-BAD can label the NAD+-consumers PARP-1 and PARP-10 in a UV-dependent manner

Methodology Applied

Scientific EffectUV-dependent labeling: Photopolymerisation

Data Source

PatentUS12441757B2Platform for screening NAD+ binding proteins in a cellular context

Publication Date: 2025.10.14 OREGON HEALTH & SCI UNIV

AI summary

Provided herein are novel compounds, compositions, that can used as clickable, photo-affinity labeling (PAL) probes methods for use in screening NAD+ binding proteins.