A computational framework for identifying novel allosteric modulators of TIMP2 and exploring mechanisms of neuroplasticity.
Please cite this work if you use or adapt the pipeline.
TIMP2 (Tissue Inhibitor of Metalloproteinase-2) regulates hippocampal plasticity and cognitive function through MMP-independent neuronal signaling.
Building on Ferreira et al. (2023, eNeuro) and integrin-mechanistic studies by Pérez-Martínez & Jaworski (2005) and Herrera-Molina et al. (2012), this project identifies a cryptic, chemically promiscuous allosteric pocket in TIMP2 and demonstrates that it accommodates both halogenated and non-halogenated scaffolds with high CNS drug-likeness.
TIMP2 modulates neural plasticity through dual integrin-dependent signaling systems that together maintain a dynamic balance between neurite growth and retraction.
- Pérez-Martínez & Jaworski (2005) showed that TIMP2 activates neuronal α3β1 integrin, stimulating the cAMP/Rap1/ERK cascade and promoting neurite outgrowth and differentiation — a growth-promoting, pro-plasticity pathway independent of metalloproteinase inhibition.
- Herrera-Molina et al. (2012) revealed that astrocytic αVβ3 integrin binds neuronal Thy-1, triggering Src inactivation and neurite retraction, defining an opposing, retractive mechanism relevant to axonal remodeling and glial responses.
- Ferreira et al. (2023) confirmed in vivo that neuronal TIMP2 is essential for hippocampal neurogenesis and memory formation, directly linking these integrin pathways to cognitive function.
Together, these findings describe a bidirectional integrin–matrix feedback loop:
TIMP2–α3β1 drives neuronal growth and synaptic plasticity, whereas Thy-1–αVβ3 constrains or reverses it during glial activation.
The cryptic allosteric site discovered in this project may stabilize TIMP2’s pro-plasticity conformation and tip this balance toward regeneration.
Proposed mechanism of action for TIMP2 allosteric modulation.
Binding of a small molecule to the cryptic N-terminal pocket (Val6, Leu100, Phe103) induces a conformational shift enhancing TIMP2’s affinity for α3β1 integrins.
This promotes downstream activation of the cAMP/Rap1/ERK pathway, leading to increased neurite outgrowth, neurogenesis, and synaptic plasticity.
References:
- Pérez-Martínez L. & Jaworski D.M. (2005). TIMP-2 promotes neuronal differentiation and neurite outgrowth through α3β1 integrin and ERK signaling. J Neurosci. 25 (26): 7997–8007.
- Herrera-Molina R. et al. (2012). The integrin αVβ3 interacts with Thy-1 and regulates neurite outgrowth in hippocampal neurons. PLoS ONE 7 (4): e34295.
- Ferreira T.A. et al. (2023). Neuronal TIMP2 regulates hippocampal neurogenesis and synaptic plasticity. eNeuro 10 (4): ENEURO.0031-23.2023.
| Step | Script | Function |
|---|---|---|
| 1️⃣ | dock_adaptive.py |
Adaptive AutoDock Vina screening with CPU benchmarking. |
| 2️⃣ | rebuild_hits.py |
Parses .pdbqt files to rebuild SMILES and docking scores. |
| 3️⃣ | timp2_triage.py |
Triage CNS/peripheral hits; energy and diversity filters. |
| 4️⃣ | timp2_analysis.py |
Integrates ADMET data, CNS MPO, and scaffold clustering. |
| 5️⃣ | add_zinc_ids_prioritized.py |
Re-maps prioritized compounds to ZINC IDs. |
| 6️⃣ | tier_1_filter.py |
Strict ADMET-AI toxicity tiers (Tier 1 = clean). |
| 7️⃣ | diversity_selection_script.py |
Balances chemical diversity across chunks. |
| 8️⃣ | singleton.py |
Identifies unique (singleton) scaffolds. |
| 9️⃣ | scaffold_extraction_rdkit.py |
Generates Murcko scaffold images. |
Hardware: Dual Xeon (24 cores, 128 GB RAM), NVMe SSD, Windows 10 Pro
Software: AutoDock Vina 1.2.5, RDKit 2023.03, OpenBabel 3.1.1, ADMET-AI v2.1, Schrödinger SiteMap (2025-2), PyMOL 2.6-3.1
Create environment:
conda env create -f environment.yml
conda activate timp2-docking
Example run:
python scripts/dock_adaptive.py data/strict_0001.smi
python scripts/rebuild_hits.py
python scripts/timp2_triage.py --hits-csv work_strict/strict_0001_hits.csv --out triage_out/strict_0001
python scripts/timp2_analysis.py triage_out/strict_0001/cns_hits.csv -o analysis_out/