Graph Convolutional Capsule Regression (GCCR): A Model for Accelerated Filtering of Novel Potential Candidates for SARS-CoV-2 based on Binding Affinity


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Abstract

Background:There has been a growing interest in discovering a viable drug for the new coronavirus (SARS-CoV-2) since the beginning of the pandemic. Protein-ligand interaction studies are a crucial step in the drug discovery process, as it helps us narrow the search space for potential ligands with high drug-likeness. Derivatives of popular drugs like Remdesivir generated through tools employing evolutionary algorithms are usually considered potential candidates. However, screening promising molecules from such a large search space is difficult. In a conventional screening process, for each ligand-target pair, there are time-consuming interaction studies that use docking simulations before downstream tasks like thermodynamic, kinetic, and electrostatic-potential evaluation.

Objective:This work aims to build a model based on deep learning applied over the graph structure of the molecules to accelerate the screening process for novel potential candidates for SARS-CoV-2 by predicting the binding energy of the protein-ligand complex.

Methods:In this work, ‘Graph Convolutional Capsule Regression’ (GCCR), a model which uses Capsule Neural Networks (CapsNet) and Graph Convolutional Networks (GCN) to predict the binding energy of a protein-ligand complex is being proposed. The model’s predictions were further validated with kinetic and free energy studies like Molecular Dynamics (MD) for kinetic stability and MM/GBSA analysis for free energy calculations.

Results:The GCCR showed an RMSE value of 0.0978 for 81.3% of the concordance index. The RMSE of GCCR converged around the iteration of just 50 epochs scoring a lower RMSE than GCN and GAT. When training with Davis Dataset, GCCR gave an RMSE score of 0.3806 with a CI score of 87.5%.

Conclusion:The proposed GCCR model shows great potential in improving the screening process based on binding affinity and outperforms baseline machine learning models like DeepDTA, KronRLS, Sim- Boost, and other Graph Neural Networks (GNN) based models like Graph Convolutional Networks (GCN) and Graph Attention Networks (GAT).

About the authors

Aravind Krishnan

Department of Computer Science and Engineering, Amrita School of Computing, Coimbatore, Amrita Vishwa Vidyapeetham,

Email: info@benthamscience.net

Dayanand Vinod

Department of Computer Science and Engineering, Amrita School of Computing, Coimbatore, Amrita Vishwa Vidyapeetham,

Author for correspondence.
Email: info@benthamscience.net

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