Module 2

PROTACs & Molecular Glues

Proteolysis-targeting chimeras (PROTACs) are heterobifunctional small molecules that recruit a target protein to an E3 ubiquitin ligase, inducing polyubiquitination and proteasomal degradation. Unlike inhibitors, PROTACs are catalytic: one molecule can degrade many target copies. This module covers the design principles, ternary complex biology, and the first approvals.

1. PROTAC Architecture

A PROTAC is three parts covalently linked:

POI ligand — small-molecule binder to the target protein (can be a weak binder because affinity is not the limiting factor).
Linker — 6–18-atom spacer optimised for geometry.
E3 ligand — typically recruits CRBN (thalidomide derivatives) or VHL; occasionally MDM2, IAP.

Upon formation of the POI-PROTAC-E3 ternary complex, the E3 catalyses polyubiquitination of the POI, which is then cleared by the 26S proteasome. Bondeson 2015 and Sakamoto 2001 introduced the concept; Arvinas, C4 Therapeutics, and Kymera have commercial pipelines.

2. Ternary Complex & Hook Effect

PROTAC efficacy is governed by the ternary complex (POI:PROTAC:E3). Cooperative ternary formation — when the POI and E3 favourably interface — amplifies activity. At high PROTAC concentrations, however, each end of the molecule saturates its partner independently, suppressing ternary formation: this is the hook effect, a bell-shaped dose-response curve that is a hallmark of all heterobifunctional degraders.

\[ [\text{POI}\cdot\text{PROTAC}\cdot\text{E3}] \propto \frac{[\text{PROTAC}]}{(K_{d1} + [\text{PROTAC}])(K_{d2} + [\text{PROTAC}])}\cdot \alpha_{coop} \]

Simulation: Hook Effect

Python

script.py31 lines

import numpy as np, matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt

# PROTAC hook effect: ternary complex vs PROTAC concentration
# At high conc, PROTAC saturates E3 and POI separately -> ternary falls
conc = np.logspace(-10, -4, 300)
Kd_E3 = 1e-8
Kd_POI = 1e-8
# Ternary = [POI:PROTAC:E3]
# Simplified one-binding at a time
frac_POI_bound = conc / (Kd_POI + conc)
frac_E3_bound = conc / (Kd_E3 + conc)
# Ternary ~ proportional to (1 - single-bound saturation overshoot)
ternary = frac_POI_bound * frac_E3_bound * np.exp(-conc/1e-6)

fig, ax = plt.subplots(figsize=(11, 5), facecolor='#0a0a1a')
ax.set_facecolor('#111827'); ax.tick_params(colors='#cbd5e1')
for s in ax.spines.values(): s.set_color('#334155')
ax.semilogx(conc*1e9, ternary, color='#2dd4bf', lw=2.6)
ax.axvline(conc[np.argmax(ternary)]*1e9, color='#fbbf24', ls='--',
           label=f'Optimal ~{conc[np.argmax(ternary)]*1e9:.0f} nM')
ax.set_xlabel('PROTAC concentration (nM)', color='#cbd5e1')
ax.set_ylabel('Ternary complex (relative)', color='#cbd5e1')
ax.set_title('Hook effect: bell-shaped dose-response',
             color='#5eead4', fontweight='bold')
ax.grid(True, color='#334155', alpha=0.3)
ax.legend(facecolor='#1e293b', edgecolor='#334155', labelcolor='#cbd5e1')
plt.tight_layout()
plt.savefig('output.png', dpi=120, bbox_inches='tight', facecolor='#0a0a1a')
print('PROTAC efficacy peaks at moderate concentration; higher doses saturate and reduce ternary complex')

Click Run to execute the Python code

Code will be executed with Python 3 on the server

3. Molecular Glues

Molecular glues are smaller (MW ~400), often drug-like molecules that stabilise a novel protein-protein interface between an E3 and a neo-substrate — no independent POI ligand. Thalidomide (CRBN) was the unrecognised first molecular glue; indisulam (Uehara 2017) redirects CRBN to RBM39. Chan 2024 machine-learning screening yielded the first rationally-designed molecular glues. These agents combine the pharmacologic advantages of small molecules with the scope-expansion of PROTACs.

4. Clinical Progress

Arvinas’ ARV-471 (vepdegestrant, ER degrader) is in Phase 3 for ER+ breast cancer. ARV-110 (AR degrader) showed Phase 1/2 activity in prostate cancer. Kymera’s KT-474 (IRAK4 degrader) is in Phase 2 for autoimmune disease. Molecular-glue degraders for GSPT1, BCL6, and RAS-GTP are in preclinical development. First PROTAC approvals are expected 2025–2027.

Key References

• Sakamoto, K. M. et al. (2001). “PROTACs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation.” Proc. Natl. Acad. Sci., 98, 8554–8559.

• Bondeson, D. P. et al. (2015). “Catalytic in vivo protein knockdown by small-molecule PROTACs.” Nat. Chem. Biol., 11, 611–617.

• Burslem, G. M. & Crews, C. M. (2020). “Proteolysis-targeting chimeras as therapeutics.” Cell, 181, 102–114.

• Uehara, T. et al. (2017). “Selective degradation of splicing factor CAPERα by anticancer sulfonamides.” Nat. Chem. Biol., 13, 675–680.

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