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Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

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High-Affinity Nanobody Against the LEDGF PWWP Domain Inhibits Chromatin Binding In Vitro.

Thibault Vantieghem¹, Sofie Jansen¹, Thatcher Zinabu Akele²

¹Biocrystallography, KU Leuven, 3000 Leuven, Belgium.

|May 27, 2026

Summary

This summary is machine-generated.

Researchers developed nanobodies targeting the LEDGF PWWP domain, crucial for HIV-1 integration and disease. One nanobody successfully disrupted LEDGF-chromatin interactions, offering new tools for drug design.

Keywords:

LEDGF/p75 PWWP domain VHH binding study chromatin reader epigenetics inhibitor nanobody protein–protein interaction single-domain antibody

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Published on: February 7, 2019

Area of Science:

Biochemistry
Structural Biology
Molecular Biology

Background:

Lens epithelium-derived growth factor p75 (LEDGF/p75) PWWP domain binds chromatin via H3K36me2/3 and DNA.
LEDGF/p75 is implicated in diseases, including HIV-1 integration, but its PWWP domain is challenging for small molecule targeting.
High-affinity nanobodies (Nbs) were generated to probe the LEDGF PWWP domain's structure and function.

Purpose of the Study:

To generate and characterize nanobodies targeting the LEDGF PWWP domain.
To investigate the structural basis of LEDGF PWWP domain interactions.
To assess the functional impact of nanobodies on LEDGF/p75 chromatin engagement.

Main Methods:

Immunization of camelids and screening of phage display libraries for high-affinity nanobodies.
Recombinant expression, purification, and characterization of nanobodies using SPR and SEC.
X-ray crystallography for structural analysis and AlphaScreen assays for functional evaluation.

Main Results:

Nine unique nanobodies were identified, with seven exhibiting nanomolar affinity for the LEDGF PWWP domain.
Structural analysis revealed canonical immunoglobulin folds, with one nanobody (NbH10) inhibiting LEDGF/p75 interaction with H3K36me3 nucleosomes.
Five nanobodies also bound the homologous HRP-2 domain, indicating conserved binding surfaces.

Conclusions:

A validated panel of nanobodies targeting the LEDGF PWWP domain was established.
One nanobody (NbH10) was shown to functionally disrupt LEDGF-chromatin interactions.
These nanobodies are valuable tools for further functional studies and structure-based drug design targeting LEDGF/p75.