Journal Article

LEADD: Lamarckian evolutionary algorithm for de novo drug design

Kerstjens, Alan, De Winter, Hans

2022

Overview

Given an objective function that predicts key properties of a molecule, goal-directed de novo molecular design is a useful tool to identify molecules that maximize or minimize said objective function. Nonetheless, a common drawback of these methods is that they tend to design synthetically unfeasible molecules. In this paper we describe a Lamarckian evolutionary algorithm for de novo drug design (LEADD). LEADD attempts to strike a balance between optimization power, synthetic accessibility of designed molecules and computational efficiency. To increase the likelihood of designing synthetically accessible molecules, LEADD represents molecules as graphs of molecular fragments, and limits the bonds that can be formed between them through knowledge-based pairwise atom type compatibility rules. A reference library of drug-like molecules is used to extract fragments, fragment preferences and compatibility rules. A novel set of genetic operators that enforce these rules in a computationally efficient manner is presented. To sample chemical space more efficiently we also explore a Lamarckian evolutionary mechanism that adapts the reproductive behavior of molecules. LEADD has been compared to both standard virtual screening and a comparable evolutionary algorithm using a standardized benchmark suite and was shown to be able to identify fitter molecules more efficiently. Moreover, the designed molecules are predicted to be easier to synthesize than those designed by other evolutionary algorithms. Graphical Abstract

• Publisher: Springer International Publishing,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Accessibility / Algorithms / Chemistry / Chemistry and Materials Science / Compatibility / Computational Biology/Bioinformatics / Computational efficiency / Computer applications / Computer Applications in Chemistry / De novo drug design / Design / Documentation and Information in Chemistry / Drug development / Evolutionary algorithm / Evolutionary algorithms / Fragment-based / Fragments / Genetic algorithms / Graph-based / Objective function / Optimization / Reproductive behavior / Research Article / Synthetic accessibility / Theoretical and Computational Chemistry