Combining High‐Throughput Synthesis and High‐Throughput Protein Crystallography for Accelerated Hit Identification

Abstract

Protein crystallography (PX) is widely used to drive advanced stages of drug optimization or to discover medicinal chemistry starting points by fragment soaking. However, recent progress in PX could allow for a more integrated role into early drug discovery. Here, we demonstrate for the first time the interplay of high throughput synthesis and high throughput PX. We describe a practical multicomponent reaction approach to acrylamides and ‐esters from diverse building blocks suitable for mmol scale synthesis on 96‐well format and on a high‐throughput nanoscale format in a highly automated fashion. High‐throughput PX of our libraries efficiently yielded potent covalent inhibitors of the main protease of the COVID‐19 causing agent, SARS‐CoV‐2. Our results demonstrate, that the marriage of in situ HT synthesis of (covalent) libraires and HT PX has the potential to accelerate hit finding and to provide meaningful strategies for medicinal chemistry projects.

Fast fragment and compound screening pipeline at the Swiss Light Source

“…The SLS MX FFCS pipeline has been in operation since 2019, with a number of successful academic collaborations and industry customer projects. At the onset of the COVID-19 pandemic the project portfolio was expanded by a Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protein target (Sutanto et al, 2021). Experience from the first FFCS campaigns clearly emphasized the importance of two crucial aspects of the pipeline: (i) DMSO optimization and (ii) software flexibility.…”

HEIDI: an experiment-management platform enabling high-throughput fragment and compound screening

“…Our Fast Fragment and Compound Screening (FFCS) facility at the Swiss Light Source (SLS) has effectively aided scientists across many campaigns (Bedi et al, 2020;Sutanto et al, 2021;Huang et al, 2024). The FFCS utilizes a Formulatrix Rock Imager to store and image crystals grown in SWISSCI 3 Lens plates (MRC3).…”

Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket

“…S1) to screen 631 fragments using the Fast Fragment and Compound Screening (FFCS) facility at the Swiss Light Source (SLS) (Kaminski et al, 2022, Stegmann et al, 2023. This open crystal form has been reported previously (Zaidman et al, 2021;Sutanto et al, 2021), but was only obtained by co-crystallization with potent, covalent inhibitors and was not previously used for fragment screening. With an overall hit rate of 4.5% (similar to that reported by COVID Moonshot), this crystal-based fragment-screening campaign identified 29 novel fragments in the active site and remote pockets of 3CL pro .…”