artificial intelligence methods for molecular property ......artificial intelligence methods for...
TRANSCRIPT
![Page 1: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/1.jpg)
Artificial Intelligence Methods for Molecular Property
PredictionEvan N. Feinberg
Pande Lab
![Page 3: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/3.jpg)
https://srconstantin.wordpress.com/2017/01/28/performance-trends-in-ai/
MNIST Performance over Time
![Page 4: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/4.jpg)
![Page 5: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/5.jpg)
Copyright Prof. Chris Manning, Stanford
http://colah.github.io/posts/2015-08-Understanding-LSTMs/
![Page 6: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/6.jpg)
What’s the right approach for molecules?
![Page 7: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/7.jpg)
Talk Part 1 Roadmap1. How to represent
molecules?
2. How to represent systems of molecules?
3. New DNNs to leverage those representations
4. Applications to Drug Pharmacokinetics and Binding Prediction
![Page 8: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/8.jpg)
Car
bon
Oxy
gen
Nitr
ogen
sp3
hyb.
sp2
hyb.
![Page 9: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/9.jpg)
Multi-Layer Perceptron /Fully Connected Neural Network
Graph Convolutional Neural Network(GCNN)
![Page 10: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/10.jpg)
Input: SP2 Hybridized Carbon
After First Hidden Layer: RNN(SP2 Hybridized Carbon,
Weights * [Primary Amine Nitrogen +Alkane Carbon with 2 Implicit Hydrogens
+ SP2 Hybridized Oxygen] )
After Second Hidden Layer: Informationhas Propagated from All Heavy Atoms
To Carbonyl Carbon
Gated GraphNeural Network(Fancy GCNN)
MessageUpdate
![Page 11: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/11.jpg)
What about two (or more!) interacting molecules?
![Page 12: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/12.jpg)
![Page 13: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/13.jpg)
Staged Spatial Graph Convolution (SSGC)
Asp
Phe
Stage 1 Stage 2
} Graph Gather+ Fully Connected LayersStage 3
Feinberg, E.N., Sur, D., Husic, B.E., Mai, D., Li, Y., Yang, J., Ramsundar, B. and Pande, V.S.,
2018. Spatial Graph Convolutions for Drug Discovery. arXiv preprint arXiv:1803.04465.
![Page 14: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/14.jpg)
Asp
Phe
Stage 1 Stage 2
} Graph Gather+ Fully Connected LayersStage 3
![Page 15: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/15.jpg)
Asp
Phe
Stage 1 Stage 2
} Graph Gather+ Fully Connected LayersStage 3
![Page 16: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/16.jpg)
Asp
Phe
Stage 1 Stage 2
} Graph Gather+ Fully Connected LayersStage 3
![Page 17: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/17.jpg)
Predicting Molecular Properties
Wu, Z., Ramsundar, B., Feinberg, E.N., Gomes, J., Geniesse, C., Pappu, A.S., Leswing, K. and Pande,
V., 2018. MoleculeNet: a benchmark for molecular machine learning. Chemical Science, 9(2), pp.513-530.
![Page 18: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/18.jpg)
Challenge 2: Ligand-based Toxicity (Tox21) Prediction
Model Architecture AUC, Valid AUC, TestRandom Forests 0.763 0.769Graph Convolution, Standard 0.825 0.829
Graph Convolution, Weave 0.828 0.820Graph Convolution, PotentialNet (Ours)
0.878 0.863
Challenge 3: Ligand-based Solubility (ESOL) Prediction
Model Architecture RMSE, Valid RMSE, TestRandom Forests 1.16 1.07Graph Convolution, Standard 1.05 0.97
Graph Convolution, Weave 0.57 0.61
Graph Convolution, PotentialNet (Ours)
0.54 0.50
Challenge 4: QM8 Electronic Property Prediction
Model Architecture MAE, Valid MAE, TestMultitask 1.55E-02 1.50E-02Graph Convolution, Standard 1.50E-02 1.48E-02
Graph Convolution, MPNN 1.46E-02 1.43E-02Graph Convolution, Staged Spatial (Ours)
1.14E-02 1.12E-02
8,014 Compounds
21,768 Compounds1,128 Compounds
Model Architecture Test Pearson RStaged Spatial Graph Convolution (Ours) 0.822 (0.021)
PotentialNet Spatial Graph Convolution 0.795 (0.040)
GGNN, Ligand-only control 0.650 (0.017)
TopologyNet (No Validation Set) 0.826
RF-Score 0.783
X-Score 0.643
Challenge 1: Protein-Ligand Binding Affinity (PDBBind)
1,300 Compounds
![Page 19: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/19.jpg)
Part 2: Harnessing Molecular Dynamics with Machine Learning to Systematically Discover Lead
Molecules
![Page 20: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/20.jpg)
Feinberg, EN, Farimani AB, Hernandez CX, Pande VS. Kinetic Machine Learning Unravels Ligand-Directed Conformational Change of μ Opioid Receptor. biorXiv. in Review. http://www.biorxiv.org/content/early/2017/07/31/170886
µ Opioid Receptor
![Page 21: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/21.jpg)
So, if Drug Targets, like GPCRs, sample many conformations….
![Page 22: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/22.jpg)
Carfentanil (Agonist)
Nalorphine (antagonist)
Ebastine (non-binder)
Carfentanil (Agonist)
Nalorphine (antagonist)
Ebastine (non-binder)
Molecular Docking
Model-Free Rank
…then why does virtual screening dock ligands to only one receptor state?
![Page 23: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/23.jpg)
tIC2
tIC1
Unliganded BU72 Sufentanil
Feinberg, EN, Farimani AB, Hernandez CX, Pande VS. Kinetic Machine Learning Unravels Ligand-Directed Conformational Change of μ Opioid Receptor. biorXiv. in Review. http://www.biorxiv.org/content/early/2017/07/31/170886
McGibbon, Robert T., Brooke E. Husic, and Vijay S. Pande. "Identification of simple reaction coordinates from complex dynamics." The Journal of Chemical Physics 146, no. 4 (2017): 044109.
MD simulations & Unsupervised ML capture salient conformations of drug target
![Page 24: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/24.jpg)
Supervised Machine Learning exploits Conformational Diversity from Molecular Simulation to Enhance the Prediction of Affinity and Efficacy
![Page 25: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/25.jpg)
![Page 26: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/26.jpg)
Stanford Compound Library (135,500 ligands)
Dock to MD States
Obtain 135,500 x 25 matrix of scores
Apply Random Forest affinity and agonism models
Collaborate with chemists at Sloan-Kettering to experimentally test
![Page 27: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/27.jpg)
![Page 28: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/28.jpg)
Carfentanil
Nalorphine Morphine
Methadone
FMP4 achieves binding and agonism at µ Opioid Receptor without a tertiary amine group
![Page 29: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/29.jpg)
Feinberg, E.N., Farimani, A.B., Uprety, R., Hunkele, A., Pasternak, G.W., Majumdar,
S. and Pande, V.S., 2018. Machine Learning Harnesses Molecular Dynamics to
Discover New mu Opioid Chemotypes. arXiv preprint arXiv:1803.04479.
Crystal Structure (5C1M)
Simulated FMP4-Specific Structure
![Page 30: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/30.jpg)
Conclusions
![Page 31: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/31.jpg)
![Page 32: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/32.jpg)
We acknowledge the generous support of Dr. Anders G. Frøseth and Mr. Christian Sundt for our work on machine learning. The Pande Group is broadly sup
Acknowledgments
![Page 33: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/33.jpg)
Acknowledgments
Vijay S. Pande
Ron O. Dror Brian Kobilka Mehrdad Shamloo Kevin Grimes
![Page 34: Artificial Intelligence Methods for Molecular Property ......Artificial Intelligence Methods for Molecular Property Prediction. Evan N. Feinberg . Pande Lab](https://reader033.vdocuments.site/reader033/viewer/2022051808/6009df70c8163146395b15ea/html5/thumbnails/34.jpg)
Acknowledgments