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PLD3 and PLD4 synthesize lysosomal S,S-BMP

ABSTRACT: LD3 knock out cells were generated in HEK293T and HMC3 cells. Proteomics was done to test if they have any significant changes in the abundance of proteins that metabolize sugar lipids like gangliosides.

INSTRUMENT(S): autoflex

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Zhuoning Li

LAB HEAD: Tobias Walther

PROVIDER: PXD046505 | Pride | 2024-10-22

REPOSITORIES: Pride

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			Action	DRS
	AddBack_HEK293T_WholeCell_1_Slot1-52_1_724.d.zip	Other
	AddBack_HEK293T_WholeCell_2_Slot1-53_1_725.d.zip	Other
	AddBack_HEK293T_WholeCell_3_Slot1-54_1_726.d.zip	Other
	AddBack_HMC3_WholeCell_1_Slot1-43_1_712.d.zip	Other
	AddBack_HMC3_WholeCell_2_Slot1-44_1_713.d.zip	Other

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PLD3 and PLD4 synthesize lysosomal S,S-BMP

Project description:This part of the data submission of PXD046505. LD3 knock out cells were generated in HEK293T and HMC3 cells. Proteomics was done to test if they have any significant changes in the abundance of proteins that metabolize sugar lipids like gangliosides.

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Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders

Project description:Small molecules that induce protein-protein interactions to exert proximity-driven pharmacology such as targeted protein degradation are a powerful class of therapeutics1-3. Molecular glues are of particular interest given their favorable size and chemical properties and represent the only clinically approved degrader drugs4-6. The discovery and development of molecular glues for novel targets, however, remains challenging. Covalent strategies could in principle facilitate molecular glue discovery by stabilizing the neo-protein interfaces. Here, we present structural and mechanistic studies that define a trans-labeling covalent molecular glue mechanism, which we term “template-assisted covalent modification”. We found that a novel series of BRD4 molecular glue degraders act by recruiting the CUL4DCAF16 ligase to the second bromodomain of BRD4 (BRD4BD2). BRD4BD2, in complex with DCAF16, serves as a structural template to facilitate covalent modification of DCAF16, which stabilizes the BRD4-degrader-DCAF16 ternary complex formation and facilitates BRD4 degradation. A 2.2 Å cryo-electron microscopy structure of the ternary complex demonstrates that DCAF16 and BRD4BD2 have pre-existing structural complementarity which optimally orients the reactive moiety of the degrader for DCAF16Cys58 covalent modification. Systematic mutagenesis of both DCAF16 and BRD4BD2 revealed that the loop conformation around BRD4His437, rather than specific side chains, is critical for BD2 selectivity. Supporting a general applicability, we find that a subset of compounds leads to a drug-induced GAK-BRD4 interaction stabilized by covalent modification of GAK. Together our work establishes “template-assisted covalent modification” as a mechanism for covalent molecular glues, which opens a new path to proximity driven pharmacology.

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