Towards De Novo Drug Design for the Coronavirus: A Drug-Target Interaction Prediction Approach using Atom-enhanced Graph Neural Network with Multi-hop Gating Mechanism

Abstract

For humans, the COVID-19 pandemic and Coronavirus have undeniably been a nightmare. Although there are effective vaccines, specific drugs are still urgent. Normally, to identify potential drugs, one needs to design and then test interactions between the drug and the virus in an in silico manner for determining candidates. This Drug-Target Interaction (DTI) process, can be done by molecular docking, which is too complicated and time-consuming for manual works. Therefore, it opens room for applying Artificial Intelligence (AI) techniques. In particular, Graph Neural Network (GNN) attracts recent attention since its high suitability for the nature of drug compounds and virus proteins. However, to introduce such a representation well-reflecting biological structures of biological compounds is not a trivial task. Moreover, since available datasets of Coronavirus are still not highly popular, the recently developed GNNs have been suffering from overfitting on them. We then address those issues by proposing a novel model known as Atom-enhanced Graph Neural Network with Multi-hop Gating Mechanism. On one hand, our model can learn more precise features of compounds and proteins. On the other hand, we introduce a new gating mechanism to create better atom representation from non-neighbor information. Once applying transfer learning from very large databanks, our model enjoys promising performance, especially when experimenting with Coronavirus.