Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design

Hassen, A.K.; Sicho, M.; Aalst, Y.J. van; Huizenga, M.C.W.; Reynolds, D.N.R.; Luukkonen, S.I.M.; Bernatavicius, A.; Clevert, D.-A.; Janssen, A.P.A.; Westen, G.J.P. van; Preuss, M.

doi:doi:10.1186/s13321-024-00910-4

Computer-Aided Synthesis Planning (CASP) and CASP-based approximated synthesizability scores have rarely been used as generation objectives in Computer-Aided Drug Design despite facilitating the in-silico generation of synthesizable molecules. However, these synthesizability approaches are disconnected from the reality of small laboratory drug design, where building block resources are limited, thus making the notion of in-house synthesizability with already available resources highly desirable. In this work, we show a successful in-house de novo drug design workflow generating active and in-house synthesizable ligands of monoglyceride lipase (MGLL). First, we demonstrate the successful transfer of CASP from 17.4 million commercial building blocks to a small laboratory setting of roughly 6000 building blocks with only a decrease of -12% in CASP success when accepting two reaction-steps longer synthesis routes on average. Next, we present a rapidly retrainable in-house...Show moreComputer-Aided Synthesis Planning (CASP) and CASP-based approximated synthesizability scores have rarely been used as generation objectives in Computer-Aided Drug Design despite facilitating the in-silico generation of synthesizable molecules. However, these synthesizability approaches are disconnected from the reality of small laboratory drug design, where building block resources are limited, thus making the notion of in-house synthesizability with already available resources highly desirable. In this work, we show a successful in-house de novo drug design workflow generating active and in-house synthesizable ligands of monoglyceride lipase (MGLL). First, we demonstrate the successful transfer of CASP from 17.4 million commercial building blocks to a small laboratory setting of roughly 6000 building blocks with only a decrease of -12% in CASP success when accepting two reaction-steps longer synthesis routes on average. Next, 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. Finally, we experimentally evaluate the synthesis and biochemical activity of three de novo candidates using their CASP-suggested synthesis routes employing 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 for de novo drug design. Scientific contribution Our core scientific contribution is the introduction of in-house de novo drug design, which enables the practical application of generative methods in small laboratories by utilizing a limited stock of available building blocks. Our fast-to-adapt workflow for in-house synthesizability scoring requires minimal computational retraining costs while supporting a high diversity of generated structures. We highlight the practicality of our approach through a comprehensive in-vitro case study that relies entirely on in-house resources, including in-silico generation, synthesis planning, and activity evaluation.Show less

Leiden University Scholarly Publications

View statistics

Documents

In Collections

Generate what you can make: achieving in-house synthesizability with readily available resources in de novo drug design