Function-based OBOC screening for the direct discovery of potent protein-protein interaction inhibitors.
6 affiliations
- 1Department of Chemistry and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH) Pohang South Korea [email protected].
- 2Department of Chemistry, Sogang University Seoul 04107 South Korea [email protected].
- 3Department of Chemistry, Pusan National University Busan 46241 South Korea [email protected].
- 4Department of Science Education, Daegu National University of Education Daegu 42411 South Korea [email protected].
- 5National Research Laboratory for Convergence Degradation Biology, Korea University Seoul South Korea.
- 6Camel Biosciences Pohang South Korea.
Abstract
Protein-protein interactions (PPIs) represent an attractive class of therapeutic targets, yet the discovery of PPI inhibitors remains challenging because PPI interfaces are typically shallow and lack well-defined binding pockets. Moreover, target binding alone does not necessarily translate into functional inhibition, as compounds can engage a target protein without disrupting its interaction with a partner, and in some cases may even stabilize the complex. Combinatorial library technologies such as one-bead-one-compound (OBOC) screening enable the exploration of vast chemical diversity, but because conventional OBOC screening selects hits based on target binding rather than biological function, it is susceptible to nonfunctional or false-positive hits. These include compounds that bind outside the functional PPI interface and therefore lack inhibitory activity, compounds that stabilize rather than disrupt the PPI, and artifacts arising from avidity, nonspecific adsorption, or physical entrapment of the target protein within the polymer bead matrix. Here, we report a function-based OBOC screening platform that establishes PPI disruption, rather than target binding, as the primary selection criterion. By integrating a FRET-based competition assay with OBOC combinatorial libraries, bead-displayed compounds are selected only when they competitively and potently displace a quencher-tagged binding partner from a preassembled target complex, ensuring that fluorescence-positive beads directly report potent, functional PPI disruption. To validate this strategy, we applied the platform to the SRC-1/STAT6 interaction by screening a stapled peptide OBOC library, directly identifying highly potent functional inhibitors. Proof-of-concept experiments using DNA-encoded beads further confirmed the compatibility of this selection strategy with DNA-encoded library technologies, which enable access to substantially larger and more diverse combinatorial libraries. Together, this work establishes a broadly applicable framework for transforming affinity-based OBOC screening into function-based screening, enabling the direct discovery of biologically active PPI inhibitors.
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BibTeX
@article{wang2026functionbased,
title = {{Function-based OBOC screening for the direct discovery of potent protein-protein interaction inhibitors.}},
author = {Hee Myeong Wang and Seungyoon Jang and Sanggil Kim and Jungyeon Kim and Deokhee Kim and Yeongju Lee and Hyun Soo Lee and Min Hyeon Shin and Hyun-Suk Lim},
journal = {RSC chemical biology},
year = {2026},
month = oct,
doi = {10.1039/d6cb00273k},
url = {https://europepmc.org/article/MED/42909228},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - Function-based OBOC screening for the direct discovery of potent protein-protein interaction inhibitors.
AU - Hee Myeong Wang
AU - Seungyoon Jang
AU - Sanggil Kim
AU - Jungyeon Kim
AU - Deokhee Kim
AU - Yeongju Lee
AU - Hyun Soo Lee
AU - Min Hyeon Shin
AU - Hyun-Suk Lim
PY - 2026
DA - 2026/10/14
JO - RSC chemical biology
DO - 10.1039/d6cb00273k
UR - https://europepmc.org/article/MED/42909228
AB - Protein-protein interactions (PPIs) represent an attractive class of therapeutic targets, yet the discovery of PPI inhibitors remains challenging because PPI interfaces are typically shallow and lack well-defined binding pockets. Moreover, target binding alone does not necessarily translate into functional inhibition, as compounds can engage a target protein without disrupting its interaction with a partner, and in some cases may even stabilize the complex. Combinatorial library technologies such as one-bead-one-compound (OBOC) screening enable the exploration of vast chemical diversity, but because conventional OBOC screening selects hits based on target binding rather than biological function, it is susceptible to nonfunctional or false-positive hits. These include compounds that bind outside the functional PPI interface and therefore lack inhibitory activity, compounds that stabilize rather than disrupt the PPI, and artifacts arising from avidity, nonspecific adsorption, or physical entrapment of the target protein within the polymer bead matrix. Here, we report a function-based OBOC screening platform that establishes PPI disruption, rather than target binding, as the primary selection criterion. By integrating a FRET-based competition assay with OBOC combinatorial libraries, bead-displayed compounds are selected only when they competitively and potently displace a quencher-tagged binding partner from a preassembled target complex, ensuring that fluorescence-positive beads directly report potent, functional PPI disruption. To validate this strategy, we applied the platform to the SRC-1/STAT6 interaction by screening a stapled peptide OBOC library, directly identifying highly potent functional inhibitors. Proof-of-concept experiments using DNA-encoded beads further confirmed the compatibility of this selection strategy with DNA-encoded library technologies, which enable access to substantially larger and more diverse combinatorial libraries. Together, this work establishes a broadly applicable framework for transforming affinity-based OBOC screening into function-based screening, enabling the direct discovery of biologically active PPI inhibitors.
SN - 2633-0679
ER -