Cryo-EM: The Resolution Revolution and Drug Discovery

Oliveira, T.M.; Beek, Lotte van; Shilliday, F. B.; Debreczeni, J.; Phillips, Chris

doi:10.1177/2472555220960401

Cited by 45 publications

(32 citation statements)

References 111 publications

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“…It often requires a lot of trial and error, for example, to find suitable constructs or conditions under which a protein is amenable to crystallization. Although recent advances in the field of electron cryo-microscopy and hybrid and integrative methods (I/HM) for structure determination have accelerated the pace of structure determination, the gap between known protein sequences and experimental protein structures continues to expand ( 6 , 8 ).…”

Section: Introductionmentioning

confidence: 99%

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Váradi

Anyango

Deshpande

et al. 2021

Nucleic Acids Research

5,138

4,191

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The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions. Powered by AlphaFold v2.0 of DeepMind, it has enabled an unprecedented expansion of the structural coverage of the known protein-sequence space. AlphaFold DB provides programmatic access to and interactive visualization of predicted atomic coordinates, per-residue and pairwise model-confidence estimates and predicted aligned errors. The initial release of AlphaFold DB contains over 360,000 predicted structures across 21 model-organism proteomes, which will soon be expanded to cover most of the (over 100 million) representative sequences from the UniRef90 data set.

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Section: Introductionmentioning

confidence: 99%

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Váradi

Anyango

Deshpande

et al. 2021

Nucleic Acids Research

5,138

4,191

View full text Add to dashboard Cite

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“…As previously mentioned, the Pascal group crystallised four of the six domains of PARP1 [ 34 ] ( Figure 1 B); although a full-length structure has not yet been obtained. Perhaps the “resolution revolution” that cryo-EM is currently undergoing may provide a solution for this problem [ 151 , 152 , 153 ]. Recently the first full-length cryo-EM structure of a PARP enzyme was published.…”

Section: Parp Hpf1 and Nucleosome Remodellingmentioning

confidence: 99%

PARP Power: A Structural Perspective on PARP1, PARP2, and PARP3 in DNA Damage Repair and Nucleosome Remodelling

Beek

McClay

Patel

et al. 2021

IJMS

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Poly (ADP-ribose) polymerases (PARP) 1-3 are well-known multi-domain enzymes, catalysing the covalent modification of proteins, DNA, and themselves. They attach mono- or poly-ADP-ribose to targets using NAD+ as a substrate. Poly-ADP-ribosylation (PARylation) is central to the important functions of PARP enzymes in the DNA damage response and nucleosome remodelling. Activation of PARP happens through DNA binding via zinc fingers and/or the WGR domain. Modulation of their activity using PARP inhibitors occupying the NAD+ binding site has proven successful in cancer therapies. For decades, studies set out to elucidate their full-length molecular structure and activation mechanism. In the last five years, significant advances have progressed the structural and functional understanding of PARP1-3, such as understanding allosteric activation via inter-domain contacts, how PARP senses damaged DNA in the crowded nucleus, and the complementary role of histone PARylation factor 1 in modulating the active site of PARP. Here, we review these advances together with the versatility of PARP domains involved in DNA binding, the targets and shape of PARylation and the role of PARPs in nucleosome remodelling.

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“…Single particle cryo-electron microscopy (cryo-EM) has undergone a so-called "resolution revolution" and has produced hundreds of cryo-EM structures of 2.5 -4.5 Å resolutions in the past 10 or so years [1][2][3][4][5][6][7][8] . Structures of many macromolecules complexed with small molecule agonists, antagonist, or modulators have been published in near-atomic resolutions 2,9 .…”

Section: Introductionmentioning

confidence: 99%

Cryo-EM Structure-guided Selection of Computed Ligand Poses to Enhance Potency in MTA-synergic Inhibition of Human Protein Arginine Methyltransferase 5

Yadav

Zhou

Yang

et al. 2021

Preprint

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The potential of using cryo-electron microscopic (cryo-EM) structures of 2.5-4.0 Å resolutions for structure-based drug design was proposed recently, but is yet to be materialized. Here we show that a 3.1 Å cryo-EM structure of protein arginine methyltransferase 5 (PRMT5) is sufficient to guide the selection of computed poses of a bound inhibitor and its redesign for much higher potency. PRMT5 is an oncogenic target and its multiple inhibitors are in clinical trials for various cancer types. However, all these PRMT5 inhibitors manifest negative cooperativity with a metabolic co-factor analog --- 2-methylthioadenosine (MTA), which is accumulated substantially in cancer patients carrying defective MTA phosphorylase (MTAP). To achieve MTA-synergetic inhibition, we obtained a pharmacophore from virtual screen and synthesized a specific inhibitor (11-2F). Cryo-EM structures of the 11-2F/MTA-bound human PRMT5: MEP50 complex and its apo form together showed that the inhibitor binding in the catalytic pocket causes a shift of the cofactor-binding site by 1.5 – 2.0 Å, disfavoring cofactor-binding and resulting in positive cooperativity between 11-2F and MTA. Coarse-grained and full-atomistic MD simulations of the ligands in their binding pockets were performed to compare computed poses of 11-2F and its redesigned analogs. Three new analogs were predicted to have much better potency. One of them, after synthesis, was ~4 fold more efficient in PRMT5 inhibition in the presence of MTA than 11-2F itself. Computational analysis also suggests strong subtype specificity of 11-2F among PRMTs. These data demonstrate the feasibility of using cryo-EM structures of near-atomic resolutions and computational analysis of ligand poses for better small molecule therapeutics.

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Cryo-EM: The Resolution Revolution and Drug Discovery

Cited by 45 publications

References 111 publications

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

PARP Power: A Structural Perspective on PARP1, PARP2, and PARP3 in DNA Damage Repair and Nucleosome Remodelling

Cryo-EM Structure-guided Selection of Computed Ligand Poses to Enhance Potency in MTA-synergic Inhibition of Human Protein Arginine Methyltransferase 5

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