Drug-Target Residence Time Profiling in Native Proteomes

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Solution Overview

Problem

Existing methods for measuring drug-target interactions are biased towards purified proteins, neglecting potential off-targets and failing to account for in vivo context, leading to inaccurate predictions of drug efficacy and side effects.

Innovation Solution

A method combining limited proteolysis with mass spectrometry (LiP-MS/DarkLiP-MS) to measure drug-residence times in a complex biological context, allowing unbiased analysis of the entire proteome for drug-target interactions.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If biophysical techniques (NMR, X-ray crystallography, FRET) are used to monitor conformational changes, then measurement precision is improved, but device complexity and ease of operation worsen due to requiring purified proteins or fluorescent probes

Engineering Contradiction:

Improveconformational change detectionVSAvoidexperimental setup complexity

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The invention extracts the conformational information from complex biological mixtures by using limited proteolysis to generate structure-dependent peptides, which are then analyzed by mass spectrometry. This removes the need for purified proteins or fluorescent probes while maintaining the ability to detect conformational changes.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The invention replaces complex biophysical measurement systems (NMR, X-ray, FRET) with a simpler mass spectrometry-based approach. Instead of using sophisticated optical or magnetic equipment, the method uses proteolytic digestion patterns detected by MS to infer conformational states.

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

2Measurement precision

If methods using purified proteins are used to measure drug-target interactions, then measurement precision is improved, but reliability worsens due to neglecting off-targets and in vivo context

Engineering Contradiction:

Improvedrug-target interaction measurementVSAvoiddrug efficacy prediction

Core Design Contradiction:

Measurement precisionVSReliability

Solution Approach 1:

The invention makes the method universally applicable to entire proteomes rather than single purified proteins. The LiP-MS approach can simultaneously analyze multiple drug-target interactions across all proteins in a complex mixture, enabling comprehensive off-target detection while maintaining measurement precision for individual targets.

Inventive Principle:

Principle #6Universality (Multi-functionality)

3Reliability

If FRET-based methods are used to monitor conformational changes in native environment, then reliability is improved, but device complexity and ease of operation worsen due to requiring fluorescent probes

Engineering Contradiction:

Improvenative environment monitoringVSAvoidprobe introduction requirement

Core Design Contradiction:

ReliabilityVSEase of operation

Solution Approach 1:

The invention removes the requirement for fluorescent probes by extracting conformational information through proteolytic fragmentation patterns. Instead of labeling proteins with fluorophores, the method uses the natural structural dependencies of protease cleavage sites to report on conformational states in native environments.

Inventive Principle:

Principle #2Taking out (Extraction)

4Reliability

If limited proteolysis is combined with mass spectrometry to analyze complex mixtures, then reliability is improved by accounting for in vivo context, but measurement precision worsens due to complex background

Engineering Contradiction:

Improvein vivo context accuracyVSAvoidsignal detection in complex mixture

Core Design Contradiction:

ReliabilityVSMeasurement precision

Solution Approach 1:

The invention segments the complex biological mixture into individual peptide fragments through limited proteolysis. By analyzing the fragmentation patterns of specific peptides rather than attempting to detect intact proteins in the complex mixture, the method achieves high measurement precision while maintaining reliability from native context.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The invention uses proteolytic peptides as intermediaries to transfer conformational information from complex biological mixtures to the mass spectrometer. These structure-dependent peptides serve as mediators that preserve native conformational information while being detectable by MS with high precision.

Inventive Principle:

Principle #24Intermediary (Mediator)

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

Enables accurate prediction of drug efficacy and side effects by quantifying drug-residence times across the proteome, prioritizing effective drug candidates and minimizing off-target interactions.

Implementation Method 1

Limited proteolysis of the complex mixture under a condition in which the at least one Target is in the original conformational state to be detected

Methodology Applied

Scientific EffectProteolysis: Hydrolysis

Implementation Method 2

analytical analysis, wherein quantitative mass spectrometry-based assays in the form of selected/parallel reaction monitoring (SRM/PRM) and/or data-independent acquisition of product ion spectra is used

Methodology Applied

Scientific EffectMass spectrometry:

Data Source

PatentUS20260086093A1Methods to determine drug target residence time and to select best drug-target candidates

Publication Date: 2026.03.26 BIOGNOSYS AG

AI summary

The present invention relates to methods for the determination of the residence time between at least one Target and at least one Ligand, optionally in their native biological context, using limited proteolysis e.g., combined with selected reaction monitoring, parallel reaction monitoring, data-independent acquisition (DIA), including Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra (SWATH) methods and the like.