|
|
--- |
|
|
license: apache-2.0 |
|
|
--- |
|
|
# moPPIt: De Novo Generation of Motif-Specific Peptide Binders via Multi-Objective Discrete Flow Matching |
|
|
|
|
|
<img src="https://cdn-uploads.huggingface.co/production/uploads/649ef40be56dc456b7a36649/2P-06_gxQ_Dv3x-i1aEWH.png" width="100%"> |
|
|
|
|
|
Targeting specific functional motifs, whether conserved viral epitopes, intrinsically disordered regions (IDRs), or fusion breakpoints, is essential for modulating protein function and protein-protein interactions (PPIs). Current design methods, however, depend on stable tertiary structures, limiting their utility for disordered or dynamic targets. Here, we present a motif-specific PPI targeting algorithm (moPPIt), a framework for the de novo generation of motif-specific peptide binders derived solely from target sequence data. The core of this approach is BindEvaluator, a transformer architecture that interpolates protein language model embeddings to predict peptide-protein binding site interactions with high accuracy (AUC = 0.97). We integrate this predictor into a novel Multi-Objective-Guided Discrete Flow Matching (MOG-DFM) framework, which steers generative trajectories toward peptides that simultaneously maximize binding affinity and motif specificity. After comprehensive in silico validation of binding and motif-specific targeting, we validate moPPIt in vitro by generating binders that strictly discriminate between the FN3 and IgG domains of NCAM1, confirming domain-level specificity, and further demonstrate precise targeting of IDRs by generating binders specific to the N-terminal disordered domain of β-catenin. In functional, disease-relevant assays, moPPIt-designed peptides targeting the GM-CSF receptor effectively block macrophage polarization. Finally, we demonstrate therapeutic utility in cell engineering, where binders directed against the tumor antigen AGR2 drive specific CAR T regulatory cell activation. In total, moPPIt serves as a purely sequence-based paradigm for controllably targeting the "undruggable" and disordered proteome. |
|
|
|
|
|
--- |
|
|
|
|
|
## 1. Google Colab Notebooks |
|
|
We provide two Google Colab notebooks to help you run and evaluate moPPIt without any local setup: |
|
|
|
|
|
- **moPPIt Colab** (generate motif-specific binders while optimizing other therapeutic-related properties): [Link](https://colab.research.google.com/drive/16n8PIwKwAiG-oDLm171BWvv-lQH0dHMg?usp=sharing) |
|
|
|
|
|
- **PeptiDerive Colab** (compute Relative Interaction Scores (RIS) for residues on the target protein): [Link](https://colab.research.google.com/drive/1aCODZ-WRwhxr-u8nEB6ZrdrhIOTz7-UF?usp=sharing) |
|
|
|
|
|
--- |
|
|
|
|
|
## 2. Command-line Usage |
|
|
You can also run **moPPIt** and **BindEvaluator** from the command line. |
|
|
|
|
|
### 2.1 Run moPPIt |
|
|
|
|
|
Example command: |
|
|
``` |
|
|
python -u moo.py \ |
|
|
--output_file './samples.csv' \ |
|
|
--length 10 \ |
|
|
--n_batches 600 \ |
|
|
--weights 1 1 1 4 4 2 \ |
|
|
--motifs '16-31,62-79' \ |
|
|
--motif_penalty \ |
|
|
--objectives Hemolysis Non-Fouling Half-Life Affinity Motif Specificity \ |
|
|
--target_protein MHVPSGAQLGLRPDLLARRRLKRCPSRWLCLSAAWSFVQVFSEPDGFTVIFSGLGNNAGGTMHWNDTRPAHFRILKVVLREAVAECLMDSYSLDVHGGRRTAAG |
|
|
``` |
|
|
|
|
|
### 2.2 Run BindEvaluator |
|
|
BindEvaluator predicts the binding sites on the target protein, given a target protein seqeunce and a binder sequence. |
|
|
|
|
|
Example command: |
|
|
``` |
|
|
python -u bindevaluator.py \ |
|
|
-target MHVPSGAQLGLRPDLLARRRLKRCPSRWLCLSAAWSFVQVFSEPDGFTVIFSGLGNNAGGTMHWNDTRPAHFRILKVVLREAVAECLMDSYSLDVHGGRRTAAG \ |
|
|
-binder YVEICRCVVC \ |
|
|
-sm ./classifier_ckpt/finetuned_BindEvaluator.ckpt \ |
|
|
-n_layers 8 \ |
|
|
-d_model 128 \ |
|
|
-d_hidden 128 \ |
|
|
-n_head 8 \ |
|
|
-d_inner 64 |
|
|
``` |
|
|
|
|
|
## Repository Authors |
|
|
[Tong Chen](mailto:chentong@seas.upenn.edu), PhD Student, University of Pennsylvania |
|
|
|
|
|
[Pranam Chatterjee](mailto:pranam@seas.upenn.edu), Assistant Professor, University of Pennsylvania |
|
|
|
|
|
Reach out to us with any questions! |
