Theoretical and Computational Chemistry

Transformer Neural Network-Based Molecular Optimization Using General Transformations



Molecular optimization aims to improve the drug profile of a starting molecule. It is a fundamental problem in drug discovery but challenging due to (i) the requirement of simultaneous optimization of multiple properties and (ii) the large chemical space to explore. Recently, deep learning methods have been proposed to solve this task by mimicking the chemist's intuition in terms of matched molecular pairs (MMPs). Although MMPs is a typical and widely used strategy by medicinal chemists, it offers limited capability in terms of exploring the space of solutions. There are more options to modify a starting molecule to achieve desirable properties, e.g. one can simultaneously modify the molecule at different places including changing the scaffold. This study trains the same Transformer architecture on different datasets. These datasets consist of a set of molecular pairs which reflect different types of transformations. Beyond MMP transformation, datasets reflecting general transformations are constructed from ChEMBL based on two approaches: Tanimoto similarity (allows for multiple modifications) and scaffold matching (allows for multiple modifications but keep the scaffold constant) respectively. We investigate how the model behavior can be altered by tailoring the dataset while keeping the same model architecture. Our results show that the models trained on differently prepared datasets transform a given starting molecule in a way that it reflects the nature of the dataset used for training the model. These models could complement each other and unlock the capability for the chemists to pursue different options for improving a starting molecule.


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Supplementary material

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Supplementary figures and tables

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