Prioritizing multiple therapeutic targets in parallel using automated DNA-encoded library screening

Abstract

The identification and prioritization of chemically tractable therapeutic targets is a significant challenge in the discovery of new medicines. We have developed a novel method that rapidly screens multiple proteins in parallel using DNA-encoded library technology (ELT). Initial efforts were focused on the efficient discovery of antibacterial leads against 119 targets from Acinetobacter baumannii and Staphylococcus aureus. The success of this effort led to the hypothesis that the relative number of ELT binders alone could be used to assess the ligandability of large sets of proteins. This concept was further explored by screening 42 targets from Mycobacterium tuberculosis. Active chemical series for six targets from our initial effort as well as three chemotypes for DHFR from M. tuberculosis are reported. The findings demonstrate that parallel ELT selections can be used to assess ligandability and highlight opportunities for successful lead and tool discovery.

PhotoAffinity Bits: A Photoaffinity-Based Fragment Screening Platform for Efficient Identification of Protein Ligands

“…A key consideration, therefore, was the contribution of the photoreactive warhead to the binding affinity. Analogues of hit PhABits were synthesised with acetyl-and butanoyl-amides in place of the photoreactive group to explore the impact this had on potency (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)Supplementary Figure 3). A decrease of less than 0.6 log units in the TR-FRET assay was observed upon truncating to the acetylamide analogues, and potency was typically recovered in the butanoylamide analogues ( Figure 2C).…”

“…6 Bindingdriven assays, such as Affinity Selection Mass Spectrometry (ASMS) and DNA Encoded Libraries (DELs) have recently been developed to accelerate ligand discovery through the efficient screening of large libraries (10 6 -10 12 compounds). [7][8][9][10][11][12][13][14][15][16] While these approaches are powerful, they employ lead-like libraries (MW>300) that generate hits that may suffer from sub-optimal ligand efficiency and can prove challenging to optimise. Additionally, the upfront investment in library generation, and sample handling, limits the accessibility of this screening strategy to the broader scientific community.…”

Kinetically guided radical-based synthesis of C(sp 3 )−C(sp 3 ) linkages on DNA

“…Both α-substituted (18-24) and β-substituted (26,27) acceptors could be employed in this protocol, providing the Giese products in excellent yields. Reactive functional groups such as aldehydes (18) and acids (19,20) were tolerated in this coupling, allowing them to serve as handles for a variety of DEL-compatible downstream functionalizations (e.g., reductive amination or amide-bond formation, respectively). Moreover, acrylates with a CH 2 SO 2 Tol in the α-position underwent elimination following radical addition (58), leading to another Michael acceptor moiety (25) and making the process amenable for iterative multicycle C-C bond forming Giese in a DEL context.…”

“…In this way, libraries of incredible size (up to >10 9 members) could be procured and screened at once (rather than one by one in traditional combinatorial chemistry) with the ultimate vision of democratizing the practice of medicinal chemistry (10)(11)(12)(13)(14)(15). The vision and principles outlined therein are only recently being realized with advances in analysis and chemoselective synthesis, setting the stage for the widespread adoption of DEL-based discovery platforms in the pharmaceutical arena (16)(17)(18)(19)(20). DNA-compatible synthesis provides exciting challenges (21)(22)(23), particularly as most traditional techniques are not amenable to the idiosyncratic requirements of such systems (24,25).…”

Denoising DNA Encoded Library Screens with Sparse Learning

“…Since the seminal paper by Clark et al 1 that saw the concept of DNA encoded libraries (DELs) reduced to practice, the technology has been gaining popularity as a novel hit discovery [2][3][4] and, more recently, target prioritization tool. 5 DELs represent large combinatorial libraries of small molecules that are typically generated using a split-and-pool methodology, with 3 to 4 cycles of chemistry providing routine access to millions or even billions of unique compounds. Unlike traditional chemical libraries, though, each compound in a DEL is attached to a sequence of DNA -the tag or barcode -that stores information on its complete synthetic history, and all DEL members are kept in a mixture.…”