DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning

Liu Xuhan; Ye Kai; van Vlijmen Herman W. T.IJzerman Adriaan P.van Westen Gerard J. P.

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DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning

机译：DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning

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摘要

Rational drug design often starts from specific scaffolds to which side chains/substituents are added or modified due to the large drug-like chemical space available to search for novel drug-like molecules. With the rapid growth of deep learning in drug discovery, a variety of effective approaches have been developed for de novo drug design. In previous work we proposed a method named DrugEx, which can be applied in polypharmacology based on multi-objective deep reinforcement learning. However, the previous version is trained under fixed objectives and does not allow users to input any prior information (i.e. a desired scaffold). In order to improve the general applicability, we updated DrugEx to design drug molecules based on scaffolds which consist of multiple fragments provided by users. Here, a Transformer model was employed to generate molecular structures. The Transformer is a multi-head self-attention deep learning model containing an encoder to receive scaffolds as input and a decoder to generate molecules as output. In order to deal with the graph representation of molecules a novel positional encoding for each atom and bond based on an adjacency matrix was proposed, extending the architecture of the Transformer. The graph Transformer model contains growing and connecting procedures for molecule generation starting from a given scaffold based on fragments. Moreover, the generator was trained under a reinforcement learning framework to increase the number of desired ligands. As a proof of concept, the method was applied to design ligands for the adenosine A(2A) receptor (A(2A)AR) and compared with SMILES-based methods. The results show that 100 of the generated molecules are valid and most of them had a high predicted affinity value towards A(2A)AR with given scaffolds.

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《journal of cheminformatics》 |2023年第1期|共14页
作者
Liu Xuhan; Ye Kai; van Vlijmen Herman W. T.IJzerman Adriaan P.van Westen Gerard J. P.;
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作者单位

Leiden Acad Ctr Drug Res;

Xi An Jiao Tong Univ;

Janssen Pharmaceut NV;

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原文格式 PDF
正文语种英语
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关键词
Deep learning; Reinforcement learning; Policy gradient; Drug design; Transformer; Multi-objective optimization; Adenosine A(2A) receptor; ADENOSINE RECEPTORS; DISCOVERY; TOOL;

DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning

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