Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application

Scapin, Giovanna; Potter, Clinton S.; Carragher, Bridget

doi:10.1016/j.chembiol.2018.07.006

Cited by 67 publications

(54 citation statements)

References 79 publications

(91 reference statements)

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“…While still technically/financially demanding, cryo-electron microscopy (cryo-EM) seems well positioned in this respect, notably due to its solution phase nature and suitability for studying high MW (usually > 100 kDa) assemblies. Critically, recent reports of prototypical cryo-EM structures at atomic resolution, along with fragment bound protein structures suggest that the gap in resolution between X-ray crystallography and cryo-EM is closing quickly [149][150][151]. NMR is another technique likely to find utility here: conformational analysis of PROTACs in solution using NMR methods has been reported [152], and could further provide information on the bound PROTAC conformation in the TC [153].…”

Section: Discussionmentioning

confidence: 99%

Current strategies for the design of PROTAC linkers: a critical review

Troup

Fallan

Baud

2020

Exploration of Targeted Anti-Tumor Therapy

185

182

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PROteolysis TArgeting Chimeras (PROTACs) are heterobifunctional molecules consisting of two ligands; an “anchor” to bind to an E3 ubiquitin ligase and a “warhead” to bind to a protein of interest, connected by a chemical linker. Targeted protein degradation by PROTACs has emerged as a new modality for the knock down of a range of proteins, with the first agents now reaching clinical evaluation. It has become increasingly clear that the length and composition of the linker play critical roles on the physicochemical properties and bioactivity of PROTACs. While linker design has historically received limited attention, the PROTAC field is evolving rapidly and currently undergoing an important shift from synthetically tractable alkyl and polyethylene glycol to more sophisticated functional linkers. This promises to unlock a wealth of novel PROTAC agents with enhanced bioactivity for therapeutic intervention. Here, the authors provide a timely overview of the diverse linker classes in the published literature, along with their underlying design principles and overall influence on the properties and bioactivity of the associated PROTACs. Finally, the authors provide a critical analysis of current strategies for PROTAC assembly. The authors highlight important limitations associated with the traditional “trial and error” approach around linker design and selection, and suggest potential future avenues to further inform rational linker design and accelerate the identification of optimised PROTACs. In particular, the authors believe that advances in computational and structural methods will play an essential role to gain a better understanding of the structure and dynamics of PROTAC ternary complexes, and will be essential to address the current gaps in knowledge associated with PROTAC design.

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Section: Discussionmentioning

confidence: 99%

Current strategies for the design of PROTAC linkers: a critical review

Troup

Fallan

Baud

2020

Exploration of Targeted Anti-Tumor Therapy

185

182

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“…Thus, we proceed as follows: for each position i in the micrograph I, we extract the corresponding patch of size (2P − 1) × (2P − 1), expand it in the discretized PSWFs as in (36), and collect the a k,q as per (34) to constitute the second-order autocorrelation of the micrograph. 5 A dierent normalization is used in [24].…”

Section: F2 Autocorrelation Derivationmentioning

confidence: 99%

Toward single particle reconstruction without particle picking: Breaking the detection limit

Bendory

Boumal

Leeb

et al. 2018

Preprint

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Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method for biological macromolecules. In a cryo-EM experiment, the microscope produces images called micrographs. Projections of the molecule of interest are embedded in the micrographs at unknown locations, and under unknown viewing directions. Standard imaging techniques rst locate these projections (detection) and then reconstruct the 3-D structure from them. Unfortunately, high noise levels hinder detection. When reliable detection is rendered impossible, the standard techniques fail. This is a problem especially for small molecules, which can be particularly hard to detect. In this paper, we propose a radically dierent approach: we contend that the structure could, in principle, be reconstructed directly from the micrographs, without intermediate detection. As a result, even small molecules should be within reach for cryo-EM. To support this claim, we setup a simplied mathematical model and demonstrate how our autocorrelation analysis technique allows to go directly from the micrographs to the sought signals. This involves only one pass over the micrographs, which is desirable for large experiments. We show numerical results and discuss challenges that lay ahead to turn this proof-of-concept into a competitive alternative to state-of-the-art algorithms.

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“…Electron microscopy (EM) has become a key technique for determining the structures of biological macromolecules at high resolution (Vinothkumar & Henderson, 2016;Quentin & Raunser, 2018;Cheng, 2015;Kü hlbrandt, 2014a;Bai et al, 2015;Scapin et al, 2018), an essential step in understanding biological processes at the molecular level. The most fundamental and ultimately insurmountable limitation of the method is radiation damage to the sample.…”

Section: Introductionmentioning

confidence: 99%