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Generate What You Can Make: Achieving in-house synthesizability with readily available resources in de novo drug design

achieving in-house synthesizability with readily available resources in de novo drug design
Authors: Alan Kai Hassen; Martin Sícho; Yorick J. van Aalst; Mirjam C. W. Huizenga; Darcy N. R. Reynolds; Sohvi Luukkonen; Andrius Bernatavicius; +4 Authors

Generate What You Can Make: Achieving in-house synthesizability with readily available resources in de novo drug design

Abstract

Molecules generated by Computer-Aided Drug Design often lack synthesizability to be valuable because Computer-Aided Synthesis Planning (CASP) and CASP-based approximated synthesizability scores have rarely been used as generation objectives, despite facilitating the in-silico generation of synthesizable molecules. Published scores approximate a general notion of CASP-based synthesizability with nearly unlimited building block resources. However, this approach is disconnected from the reality of small laboratory drug design, where building block resources are limited, making a notion of in-house synthesizability that uses already available resources highly desirable. In this work, we show a successful de novo drug design workflow generating active and in-house synthesizable ligands of monoglyceride lipase (MGLL). We demonstrate the successful transfer of CASP from 17.4 million commercial building blocks to a small laboratory setting of roughly 6,000 building blocks with only a decrease of -12% in CASP success. Moreover, we present a rapidly retrainable in-house synthesizability score, successfully capturing our in-house synthesizability without relying on external building block resources. We show that including our in-house synthesizability score in a multi-objective de novo drug design workflow, alongside a simple QSAR model, provides thousands of potentially active and easily in-house synthesizable molecules. Further, we highlight differences between general and in-house synthesizability scores and demonstrate potential problems with the out-of-distribution predictive performance of synthesizability scores on generated molecules. Finally, we experimentally evaluate the synthesis and biochemical activity of three de novo candidates using their CASP-suggested synthesis routes using only in-house building blocks. We find one candidate with evident activity, suggesting potential new ligand ideas for MGLL inhibitors while showcasing the usefulness of our in-house synthesizability score.

Country
Netherlands
Keywords

Virtual screening, Synthesizability, Research, Medicinal chemistry, Information technology, T58.5-58.64, Retrosynthesis, Chemistry, In vitro, Computer-aided synthesis planning, Casp, De novo drug design, QD1-999, Synthesizability score

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    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    9
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
9
Top 10%
Average
Top 10%
Green
gold
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