# Neutron encoded activity based probes

> **NIH NIH R01** · BAYLOR COLLEGE OF MEDICINE · 2020 · $440,000

## Abstract

Drugs are designed to modulate the function of a critical protein involved in a disease; however, almost all small
molecules have off-targets which can mitigate or altogether terminate their therapeutic efficacy. Unfortunately,
there are no general methods that can identify all the protein targets that a drug binds to in an unbiased manner.
For example, Histone Deacetylase Inhibitors (HDACIs) show promising clinical activity in many diseases;
however, they are generally of low to moderate specificity and may act in part through, or be hindered by,
uncharacterized off-target interactions. We propose a strategy that will allow for rapid and deep
pharmacological profiling of early drug candidates that 1) identifies protein targets with extraordinary
confidence, 2) localizes the precise site of interaction often with amino acid residue specificity, 3) is robust against
metabolic alterations, 4) distinguishes the pharmacology of metabolites, 5) quantitates differences in
pharmacological activity between cellular contexts. With this approach we will quantitate all interactions that
each inhibitor has with proteins in a living cell. An neutron-encoded ‘bar code’ is added to activity-based
probes during a click capture and release that allows us to blindly trace the drug in a nominal mass independent
manner and simultaneously introduce quantitation channels. The barcodes are revealed in the isotopic fine
structure by high resolution mass spectrometry yet do not compromise sensitivity at lower resolution
fragmentation spectra. The neutron bar code is implemented by moving neutrons between elements and results
in a prescribed pattern of relativistic nuclear mass defects embedded in the framework of a small molecule. With
this method we can confidently retrieve drug-protein reaction products from in vivo systems regardless of
metabolic alterations to the HDAC inhibitors, measure a pharmacological profile and determine molecular
mechanism of action. Our central hypothesis is that neutron encoded activity based probe pharmacological
profiling combined with innovative fragment-based discovery to generate selective HDACIs will enable the
generation of a library of highly characterized and diversely selective HDACI probes. This will be realized through
three specific aims: in aim 1 we will employ a novel and systematically diverse group of sp3-enriched fragments
to generate HDACIs that sample the rim region of HDACs leading to highly selective interactions. In aim 2 we
will measure the pharmacological profile of our novel HDACi’s and their effect on histone acetylation. In aim 3,
we will develop a multiplexed barcoding system which to enable higher detection and resolution of drug targets
over the entire proteome. This overcomes many challenges universal to early stage drug development
efforts that have frustrated the development of specific HDAC inhibitors in particular. Although HDACIs
will be the general focus of this proposal our method is general for drug d...

## Key facts

- **NIH application ID:** 10073058
- **Project number:** 1R01GM139295-01
- **Recipient organization:** BAYLOR COLLEGE OF MEDICINE
- **Principal Investigator:** Damian Winston Young
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $440,000
- **Award type:** 1
- **Project period:** 2020-09-01 → 2025-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10073058

## Citation

> US National Institutes of Health, RePORTER application 10073058, Neutron encoded activity based probes (1R01GM139295-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10073058. Licensed CC0.

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