Work journal for Ugi GNN project

Using learnt embeddings from GNNs pretrained on docking scores to predict pIC50 for enrichment. Two cases are considered: Compounds from the Ugi reaction as SARS-CoV-2 Mpro inhibitors, as well as <insert protein target here.>

Backlog

• Write tests for data loading and other utility functions
• Decouple scripts
  • genfps
  • training
• Weigh data by dockscore - how much of a difference does it make to the model performance?
• Begin model training

Log

11 Mar - Consider downsampling dataset to 10M or even 1M; start training a 100M model in the background in the meantime. Better to see 100M molecules once than 1M 100 times? Not sure - anyhow should focus on Dopamine D4 because beta-lacatmase has a lot of covalent inhibitors so trying to benchmark with ChEMBL compounds will be very messy - should start scraping for D4 and show Alpha some examples so we can start working on filters.

7 Mar - Code mostly decoupled, ran test confirming that my current script is MUCH slower than benchmark (GPU 1min / CPU 4mins per epoch of HIV vs reported 2.5s!) - couldn't get line profiler working but suspect the issue is with on-the-fly featurisation ; should attempt multithread next

2 Mar - Tested preprocessing of graphs, completely unfeasible: 12M .csv mapped to 2.3G of .bin graphs, will have to implement multithread instead.

1 Mar - Wrote notebooks to visualise ultra-large docking datasets, pickled slightly preprocessed dataframes for fast loading, began thinking about starting training

28 Feb - Downloaded CDK2 dataset of IC50s (Alpha will ask John Chodera to dock) and I have downloaded datasets from Stoichet Nature paper on Ultra-Large docking to D4 Dopamine receptor and AmpC beta-lactamase.

Workflow for Ugi compounds

flowchart TD

subgraph Docking
Library(Ugi Library) -- OpenEye --> Conformers
Conformers -- ChemGauss4 --> DockScore(Pose Selection & Dock Score)
Library --> Preprocessing(Removal of stereochemistry/tautomers)
DockScore --> Preprocessing
Preprocessing --> PretrainSet(Pre-Training Set)
end

subgraph "MPro Inhibition"
Ugi(Synthesized Compounds) --> Activity(pIC50 Activity Measurement)
Activity ---> Trainset(Training Set)
Activity --> CompSplit(Component Split)
end


subgraph "Screening Library"
Enumeration(Ugi Enumeration from Building Blocks) --> Lib(Synthesizable Library)
end

subgraph Model
PretrainSet <== Pre-Training ==> MPNN
MPNN -- "Learnt Embedding" --> RF(Random Forest)
Trainset ----> RF
end

RF --> LeadOpt
Lib ----> LeadOpt(Scaffold Opimisation)
CompSplit --> Enrichment
RF --> Enrichment

Loading

Datasets

The datasets used in this work all consist of compounds generated from the Ugi reaction:

This one-step reaction reaction allows rapid construction of a virtual screening library by enumerating each of the four reactants (carboxylic acid, amine, ketone/aldehyde, isocyanide).

A 7.2M library of Ugi compounds comprising 263 carboxylic acids, 4215 amines, 30 aldehydes, 363 isocyanides (non-uniformly sampled) was docked against the SARS-CoV-2 Mpro receptor, and the docking scores were used to pre-train a GNN for down-stream prediction of protein binding. Tautomers and stereoisomers were enumerated for each compound, each giving different docking scores and expanding the dataset size to ~17M datapoints. The lowest (mean?) dock score for the generic smiles of the compound was used as the target value.

For training of a model for protein binding, inhibition data recorded from synthesized Ugi compounds from the COVID Moonshot project was used. These compounds are generated by holding three components of the Ugi reaction fixed and "exploring" along one of the axes. For evaluation of the trained model, instead of random splits of the training data a "component split" was performed. In this form of splitting, the held-out evaluation set is an exploration along one of the axes to assess the ability of the model to perform SAR analysis (measured via enrichment).

After the model was trained, exploratory scaffold optimisation was performed by virtually screening libraries constructed to explore along Ugi component directions. Based on medical chemistry expertise regarding binding of the compounds to the binding site, it was determined that the amine and acid components were most promising for optimisation. The most potent Ugi scaffold was taken and its components swapped with convenient & commercially available carboxylic acid and amine building blocks to construct screening libraries of size 198+344 (p4_picks) & 4008 (amine_products).

Molecular Docking

The following is the description provided from the Chodera lab about the workflow and scripts used to perform the constrained docking of the Ugi library. The files in question are kept in docking_files, also containing scripts for further preprocessing of the generated files (conversion from .bz2 to .sdf, extraction of SMILES/dock_score as .csv, concatenation of the chunks.)

Manifest

• total_ugi_library.csv - the Ugi library (SMILES)
• dock-all-chunks.sh - LSF script to dock chunks of the library
• dock-chunk.py - Python script to dock single chunk
• combine-chunks.py - Python script to combine chunks (don't use this!)
• convert-chunk.py - Python script to convert .oeb docked chunk into .sdf.bz2
• convert-all-chunks.py - Python script to convert all chunks from .oeb in output/ to .sdf.bz2 in docked/
• environment.yml - Python conda environment
• receptors/ - N0050 receptor generated in fah_prep
  • receptors/dimer/Mpro-N0050-protein.pdb is the reference protein structure used for docking
  • receptors/dimer/Mpro-N0050-ligand.mol2 is the reference ligand structure
• output/ - docked chunks in .oeb format
• docked/ - docked chunks in .sdf.bz2 format

Methodology for Molecular Docking

• The Fragalysis X-ray structure P0030 was used for protein and ligand reference structure.
• An OpenEye OEReceptor was generated using the OpenEye SpruceTK (as implemented in the fah_prep pipeline) to prepare the un-aligned structure for docking, modeling the dimer with neutral catalytic dyad.
• Next, the OpenEye toolkit was used to expand protonation states and tautomers, and then unspecified stereochemistry.
• OpenEye Omega was used to expand conformers while holding the region of the virtual compound matching the SMARTS pattern C(=O)NCC(=O)N fixed to the reference ligand structure.
• The resulting conformers were superimposed onto matching atoms of the reference compound in the reference receptor structure, and the top 10% of poses with shape overlap to the reference compound were retained.
• The top score from the resulting poses, as determined by Chemgauss4 (which accounts for steric and other interactions), was selected as the top-scoring pose for that protonation, tautomeric, and stereoisomer state and written out.
• The OpenEye Python Toolkit 2020.2.2 was used throughout.