Discovery, SAR, and X-ray Binding Mode Study of BCATm Inhibitors from a Novel DNA-Encoded Library

Deng, Hongfeng; Zhou, Jia; Sundersingh, Flora; Summerfield, Jennifer; Somers, Don O.; Messer, Jeffrey A.; Satz, Alexander L.; Ancellin, Nicolas; Arico-Muendel, Christopher C.; Bedard, Katie L Sargent; Beljean, Arthur; Belyanskaya, Svetlana; Bingham, Ryan P.; Smith, Sarah E.; Boursier, Eric; Carter, Paul; Centrella, Paolo A.; Clark, Matthew; Chung, Chun‐wa; Davie, Christopher P.; DeLorey, Jennifer L.; Ding, Yun; Franklin, G Joseph; Grady, LaShadric C.; Herry, Kenny; Hobbs, Clare I.; Kollmann, Christopher; Morgan, Barry A.; Kaushansky, Laura J.; Zhou, Quan

doi:10.1021/acsmedchemlett.5b00179

Cited by 70 publications

(92 citation statements)

References 18 publications

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“…7,15−17 Using DNA, it is possible to prepare large and structurally complex compound collections, encoding myriad structures and thereby accessing diverse chemical space. 18−20 Importantly, DEL screening output can be analyzed by highly parallel next-generation DNA sequencing (NGS), 17,21 revealing hit homology 22−24 and guiding selection of structural families for lower throughput synthesis and validation. Adaptation of DEL to solid-phase libraries 25 provides additional certainty to hit prioritization via reproducibility.…”

Section: Introductionmentioning

confidence: 99%

Poisson Statistics of Combinatorial Library Sampling Predict False Discovery Rates of Screening

MacConnell

Paegel

2017

ACS Comb. Sci.

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Microfluidic droplet-based screening of DNA-encoded one-bead-one-compound combinatorial libraries is a miniaturized, potentially widely distributable approach to small molecule discovery. In these screens, a microfluidic circuit distributes library beads into droplets of activity assay reagent, photochemically cleaves the compound from the bead, then incubates and sorts the droplets based on assay result for subsequent DNA sequencing-based hit compound structure elucidation. Pilot experimental studies revealed that Poisson statistics describe nearly all aspects of such screens, prompting the development of simulations to understand system behavior. Monte Carlo screening simulation data showed that increasing mean library sampling (ε), mean droplet occupancy, or library hit rate all increase the false discovery rate (FDR). Compounds identified as hits on k > 1 beads (the replicate k class) were much more likely to be authentic hits than singletons (k = 1), in agreement with previous findings. Here, we explain this observation by deriving an equation for authenticity, which reduces to the product of a library sampling bias term (exponential in k) and a sampling saturation term (exponential in ε) setting a threshold that the k-dependent bias must overcome. The equation thus quantitatively describes why each hit structure’s FDR is based on its k class, and further predicts the feasibility of intentionally populating droplets with multiple library beads, assaying the micromixtures for function, and identifying the active members by statistical deconvolution.

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Section: Introductionmentioning

confidence: 99%

Poisson Statistics of Combinatorial Library Sampling Predict False Discovery Rates of Screening

MacConnell

Paegel

2017

ACS Comb. Sci.

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“…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.…”

Section: Introductionmentioning

confidence: 99%

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

Grant

Fallon²,

Hann

et al. 2020

Preprint

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<p>Advances in genomic analyses enable the identification of new proteins that are associated with disease. To validate these targets, tool molecules are required to demonstrate that a ligand can have a disease-modifying effect. Currently, as tools are reported for only a fraction of the proteome, platforms for ligand discovery are essential to leverage insights from genomic analyses. Fragment screening offers an efficient approach to explore chemical space, however, it remains challenging to develop techniques that are both sufficiently high-throughput and sensitive. We present a fragment screening platform, termed PhABits (PhotoAffinity Bits), which utilises a library of photoreactive fragments to covalently capture fragment-protein interactions. Hits can be profiled to determine potency and site of crosslinking, and subsequently developed as reporters in a competitive displacement assay to identify novel hit matter. We envision that the PhABits will be widely applicable to novel protein targets, identifying starting points in the development of therapeutics.<br></p>

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“…5). Amplex red (Invitrogen, Paisley, UK) was initially diluted to 20 mM in DMSO.BCATm and L-GOX protein were cloned, expressed, and isolated in house (GSK, Stevenage, UK).…”

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confidence: 99%

Structurally Diverse Mitochondrial Branched Chain Aminotransferase (BCATm) Leads with Varying Binding Modes Identified by Fragment Screening

et al. 2016

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Inhibitors of mitochondrial branched chain aminotransferase (BCATm), identified using fragment screening, are described. This was carried out using a combination of STD-NMR, thermal melt (Tm), and biochemical assays to identify compounds that bound to BCATm, which were subsequently progressed to X-ray crystallography, where a number of exemplars showed significant diversity in their binding modes. The hits identified were supplemented by searching and screening of additional analogues, which enabled the gathering of further X-ray data where the original hits had not produced liganded structures. The fragment hits were optimized using structure-based design, with some transfer of information between series, which enabled the identification of ligand efficient lead molecules with micromolar levels of inhibition, cellular activity, and good solubility.

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Discovery, SAR, and X-ray Binding Mode Study of BCATm Inhibitors from a Novel DNA-Encoded Library

Cited by 70 publications

References 18 publications

Poisson Statistics of Combinatorial Library Sampling Predict False Discovery Rates of Screening

Poisson Statistics of Combinatorial Library Sampling Predict False Discovery Rates of Screening

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

Structurally Diverse Mitochondrial Branched Chain Aminotransferase (BCATm) Leads with Varying Binding Modes Identified by Fragment Screening

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