Imperial College London

Prof Ed Tate

Faculty of Natural SciencesDepartment of Chemistry

GSK Chair in Chemical Biology
 
 
 
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Contact

 

+44 (0)20 7594 3752e.tate Website CV

 
 
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Assistant

 

Ms Agnes Lee +44 (0)20 7594 9852

 
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Location

 

301BMolecular Sciences Research HubWhite City Campus

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Summary

 

Publications

Publication Type
Year
to

239 results found

Ritzefeld M, Zhang L, Xiao Z, Andrei S, Gavriil E, Siebold C, Lanyon-Hogg T, Tate Eet al., 2024, Design, synthesis and evaluation of inhibitors of hedgehog acyltransferase, Journal of Medicinal Chemistry, Vol: 67, Pages: 1061-1078, ISSN: 0022-2623

Hedgehog signaling is involved in embryonic development and cancer growth. Functional activity of secreted Hedgehog signaling proteins is dependent on N-terminal palmitoylation, making the palmitoyl transferase Hedgehog acyltransferase (HHAT), a potential drug target and a series of 4,5,6,7-tetrahydrothieno[3,2-c]pyridines have been identified as HHAT inhibitors. Based on structural data, we designed and synthesized 37 new analogues which we profiled alongside 13 previously reported analogues in enzymatic and cellular assays. Our results show that a central amide linkage, a secondary amine, and (R)-configuration at the 4-position of the core are three key factors for inhibitory potency. Several potent analogues with low- or sub-μM IC50 against purified HHAT also inhibit Sonic Hedgehog (SHH) palmitoylation in cells and suppress the SHH signaling pathway. This work identifies IMP-1575 as the most potent cell-active chemical probe for HHAT function, alongside an inactive control enantiomer, providing tool compounds for validation of HHAT as a target in cellular assays.

Journal article

Shah R, De Vita E, Sathyamurthi P, Conole D, Zhang X, Fellows E, Dickinson E, Fleites C, Queisser M, Harling J, Tate Eet al., 2024, Structure-guided design and optimization of covalent VHL-targeted sulfonyl fluoride PROTACs, Journal of Medicinal Chemistry, ISSN: 0022-2623

Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules that have emerged as a therapeutic modality to induce targeted protein degradation (TPD) by harnessing cellular proteolytic degradation machinery. PROTACs which ligand the E3 ligase in a covalent manner have attracted intense interest, however, covalent PROTACs with a broad protein of interest (POI) scope have proven challenging to discover by design. Here, we report structure-guided design and optimization of Von Hippel-Lindau (VHL) protein-targeted sulfonyl fluorides which covalently bind Ser110 in the HIF1α binding site. We demonstrate that their incorporation in bifunctional degraders induces targeted protein degradation of BRD4 or androgen receptor (AR) without further linker optimization. Our study discloses the first covalent VHL ligands which can be implemented directly in bifunctional degrader design expanding the substrate scope of covalent E3 ligase PROTACs.

Journal article

Ocasio CA, Baggelaar MP, Sipthorp J, Losada de la Lastra A, Tavares M, Volarić J, Soudy C, Storck EM, Houghton JW, Palma-Duran SA, MacRae JI, Tomić G, Carr L, Downward J, Eggert US, Tate EWet al., 2024, A palmitoyl transferase chemical-genetic system to map ZDHHC-specific S-acylation, Nature Biotechnology, ISSN: 1087-0156

The 23 human zinc finger Asp-His-His-Cys motif-containing (ZDHHC) S-acyltransferases catalyze long-chain S-acylation at cysteine residues across an extensive network of hundreds of proteins important for normal physiology or dysregulated in disease. Here we present a technology to directly map the protein substrates of a specific ZDHHC at the whole-proteome level, in intact cells. Structure-guided engineering of paired ZDHHC 'hole' mutants and 'bumped' chemically tagged fatty acid probes enabled probe transfer to specific protein substrates with excellent selectivity over wild-type ZDHHCs. Chemical-genetic systems were exemplified for five human ZDHHCs (3, 7, 11, 15 and 20) and applied to generate de novo ZDHHC substrate profiles, identifying >300 substrates and S-acylation sites for new functionally diverse proteins across multiple cell lines. We expect that this platform will elucidate S-acylation biology for a wide range of models and organisms.

Journal article

McHugh D, Sun B, Gutierrez-Muñoz C, Hernández-González F, Mellone M, Guiho R, Duran I, Pombo J, Pietrocola F, Birch J, Kallemeijn WW, Khadayate S, Dharmalingam G, Vernia S, Tate EW, Martínez-Barbera JP, Withers DJ, Thomas GJ, Serrano M, Gil Jet al., 2023, COPI vesicle formation and N-myristoylation are targetable vulnerabilities of senescent cells, Nature Cell Biology, Vol: 25, Pages: 1804-1820, ISSN: 1465-7392

Drugs that selectively kill senescent cells (senolytics) improve the outcomes of cancer, fibrosis and age-related diseases. Despite their potential, our knowledge of the molecular pathways that affect the survival of senescent cells is limited. To discover senolytic targets, we performed RNAi screens and identified coatomer complex I (COPI) vesicle formation as a liability of senescent cells. Genetic or pharmacological inhibition of COPI results in Golgi dispersal, dysfunctional autophagy, and unfolded protein response-dependent apoptosis of senescent cells, and knockdown of COPI subunits improves the outcomes of cancer and fibrosis in mouse models. Drugs targeting COPI have poor pharmacological properties, but we find that N-myristoyltransferase inhibitors (NMTi) phenocopy COPI inhibition and are potent senolytics. NMTi selectively eliminated senescent cells and improved outcomes in models of cancer and non-alcoholic steatohepatitis. Our results suggest that senescent cells rely on a hyperactive secretory apparatus and that inhibiting trafficking kills senescent cells with the potential to treat various senescence-associated diseases.

Journal article

Conole D, Cao F, Am Ende CW, Xue L, Kantesaria S, Kang D, Jin J, Owen D, Lohr L, Schenone M, Majmudar JD, Tate EWet al., 2023, Discovery of a potent deubiquitinase (DUB) small molecule activity‐based probe enables broad spectrum DUB activity profiling in living cells, Angewandte Chemie International Edition, Vol: 62, ISSN: 1433-7851

Deubiquitinases (DUBs) are a family of >100 proteases that hydrolyze isopeptide bonds linking ubiquitin to protein substrates. This leads to reduced substrate degradation through the ubiquitin proteasome system. Deregulation of DUB activity has been implicated in many diseases, including cancer, neurodegeneration and auto-inflammation, and several have been recognized as attractive targets for therapeutic intervention. Ubiquitin-derived covalent activity-based probes (ABPs) provide a powerful tool for DUB activity profiling, but their large recognition element impedes cellular permeability and presents an unmet need for small molecule ABPs which can account for regulation of DUB activity in intact cells or organisms. Here, through comprehensive chemoproteomic warhead profiling, we identify cyanopyrrolidine (CNPy) probe IMP-2373 (12) as a small molecule pan-DUB ABP to monitor DUB activity in physiologically relevant live cells. Through proteomics and targeted assays, we demonstrate that IMP-2373 quantitatively engages more than 35 DUBs across a range of non-toxic concentrations in diverse cell lines. We further demonstrate its application to quantification of changes in intracellular DUB activity during pharmacological inhibition and during MYC deregulation in a model of B cell lymphoma. IMP-2373 thus offers a complementary tool to ubiquitin ABPs to monitor dynamic DUB activity in the context of disease-relevant phenotypes.

Journal article

Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian Ret al., 2023, Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders., Brain

The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midb

Journal article

Liu L, Gray JL, Tate EW, Yang Aet al., 2023, Bacterial enzymes: powerful tools for protein labeling, cell signaling, and therapeutic discovery., Trends Biotechnol, Vol: 41, Pages: 1385-1399

Bacteria have evolved a diverse set of enzymes that enable them to subvert host defense mechanisms as well as to form part of the prokaryotic immune system. Due to their unique and varied biochemical activities, these bacterial enzymes have emerged as key tools for understanding and investigating biological systems. In this review, we summarize and discuss some of the most prominent bacterial enzymes used for the site-specific modification of proteins, in vivo protein labeling, proximity labeling, interactome mapping, signaling pathway manipulation, and therapeutic discovery. Finally, we provide a perspective on the complementary advantages and limitations of using bacterial enzymes compared with chemical probes for exploring biological systems.

Journal article

Huang X, Yao J, Liu L, Chen J, Mei L, Huangfu J, Luo D, Wang X, Lin C, Chen X, Yang Y, Ouyang S, Wei F, Wang Z, Zhang S, Xiang T, Neculai D, Sun Q, Kong E, Tate EW, Yang Aet al., 2023, S-acylation of p62 promotes p62 droplet recruitment into autophagosomes in mammalian autophagy, Molecular Cell, Vol: 83, Pages: 3485-3501.E11, ISSN: 1097-2765

p62 is a well-characterized autophagy receptor that recognizes and sequesters specific cargoes into autophagosomes for degradation. p62 promotes the assembly and removal of ubiquitinated proteins by forming p62-liquid droplets. However, it remains unclear how autophagosomes efficiently sequester p62 droplets. Herein, we report that p62 undergoes reversible S-acylation in multiple human-, rat-, and mouse-derived cell lines, catalyzed by zinc-finger Asp-His-His-Cys S-acyltransferase 19 (ZDHHC19) and deacylated by acyl protein thioesterase 1 (APT1). S-acylation of p62 enhances the affinity of p62 for microtubule-associated protein 1 light chain 3 (LC3)-positive membranes and promotes autophagic membrane localization of p62 droplets, thereby leading to the production of small LC3-positive p62 droplets and efficient autophagic degradation of p62-cargo complexes. Specifically, increasing p62 acylation by upregulating ZDHHC19 or by genetic knockout of APT1 accelerates p62 degradation and p62-mediated autophagic clearance of ubiquitinated proteins. Thus, the protein S-acylation-deacylation cycle regulates p62 droplet recruitment to the autophagic membrane and selective autophagic flux, thereby contributing to the control of selective autophagic clearance of ubiquitinated proteins.

Journal article

White MEH, Gil J, Tate EW, 2023, Proteome-wide structural analysis identifies warhead- and coverage-specific biases in cysteine-focused chemoproteomics, Cell Chemical Biology, Vol: 30, Pages: 828-838.e4, ISSN: 2451-9456

Covalent drug discovery has undergone a resurgence over the past two decades and reactive cysteine profiling has emerged in parallel as a platform for ligand discovery through on- and off-target profiling; however, the scope of this approach has not been fully explored at the whole-proteome level. We combined AlphaFold2-predicted side-chain accessibilities for >95% of the human proteome with a meta-analysis of eighteen public cysteine profiling datasets, totaling 44,187 unique cysteine residues, revealing accessibility biases in sampled cysteines primarily dictated by warhead chemistry. Analysis of >3.5 million cysteine-fragment interactions further showed that hit elaboration and optimization drives increased bias against buried cysteine residues. Based on these data, we suggest that current profiling approaches cover a small proportion of potential ligandable cysteine residues and propose future directions for increasing coverage, focusing on high-priority residues and depth. All analysis and produced resources are freely available and extendable to other reactive amino acids.

Journal article

Voisin TB, Couves EC, Tate EW, Bubeck Det al., 2023, Dynamics and Molecular Interactions of GPI-Anchored CD59, TOXINS, Vol: 15

Journal article

Xiao Z, Gray JL, Tate EW, 2023, Weaponizing the proteasome to overcome antimalarial drug resistance, CELL CHEMICAL BIOLOGY, Vol: 30, Pages: 415-417, ISSN: 2451-9456

Journal article

Zhang J, Lueg GA, Faronato M, Poon E, Gorelik A, Grocin AG, Caamano-Gutierrez E, Falciani F, Solari R, Carr R, Bell AS, Bartlett E, Hutton J, Llorian-Sopena M, Chakravarty P, Brzezicha B, Janz M, Garnett MJ, Chesler L, Calado DP, Tate EWet al., 2023, Dysregulation of MYC-family proteins sensitizes cancers to NMT inhibition: identification of NMTi sensitivity and mechanism, 114th Annual Meeting of the American Association for Cancer Research (AACR), Publisher: AMER ASSOC CANCER RESEARCH, ISSN: 0008-5472

Conference paper

Kallemeijn WW, Spear S, Walton J, Bussi C, Soudy C, Flynn HR, Skehel M, Carling D, Solari R, McNeish IA, Tate EWet al., 2023, From foe to friend: <i>In vivo</i> reprogramming of tumor-associated macrophages to an anti-cancer phenotype by modulating <i>N</i>-myristoyltransferase activity, 114th Annual Meeting of the American Association for Cancer Research (AACR), Publisher: AMER ASSOC CANCER RESEARCH, ISSN: 0008-5472

Conference paper

Fedoryshchak ROO, Gorelik A, Shen M, Shchepinova MMM, Perez-Dorado I, Tate EWWet al., 2023, Discovery of lipid-mediated protein-protein interactions in living cells using metabolic labeling with photoactivatable clickable probes, CHEMICAL SCIENCE, Vol: 14, Pages: 2419-2430, ISSN: 2041-6520

Journal article

Ledger E, Lau K, Tate E, Edwards Aet al., 2023, XerC is required for the repair of antibiotic- and immune-mediated DNA damage in staphylococcus aureus, Antimicrobial Agents and Chemotherapy, Vol: 67, Pages: 1-11, ISSN: 0066-4804

To survive in the host environment, pathogenic bacteria need to be able to repair DNA damage caused by both antibiotics and the immune system. The SOS response is a key bacterial pathway to repair DNA double-strand breaks and may therefore be a good target for novel therapeutics to sensitize bacteria to antibiotics and the immune response. However, the genes required for the SOS response in Staphylococcus aureus have not been fully established. Therefore, we carried out a screen of mutants involved in various DNA repair pathways to understand which were required for induction of the SOS response. This led to the identification of 16 genes that may play a role in SOS response induction and, of these, 3 that affected the susceptibility of S. aureus to ciprofloxacin. Further characterization revealed that, in addition to ciprofloxacin, loss of the tyrosine recombinase XerC increased the susceptibility of S. aureus to various classes of antibiotics, as well as to host immune defenses. Therefore, the inhibition of XerC may be a viable therapeutic approach to sensitize S. aureus to both antibiotics and the immune response.

Journal article

Bubeck D, Couves E, Gardner S, Voisin T, Bickel J, Stansfeld P, Tate Eet al., 2023, Structural basis for membrane attack complex inhibition by CD59, Nature Communications, Vol: 14, Pages: 1-13, ISSN: 2041-1723

CD59 is an abundant immuno-regulatory receptor that protects human cells from damage during complement activation. Here we show how the receptor binds complement proteins C8 and C9 at the membrane to prevent insertion and polymerization of membrane attack complex (MAC) pores. We present cryo-electron microscopy structures of two inhibited MAC precursors known as C5b8 and C5b9. We discover that in both complexes, CD59 binds the pore-forming β-hairpins of C8 to form an intermolecular β-sheet that prevents membrane perforation. While bound to C8, CD59 deflects the cascading C9 β-hairpins, rerouting their trajectory into the membrane. Preventing insertion of C9 restricts structural transitions of subsequent monomers and indirectly halts MAC polymerization. We combine our structural data with cellular assays and molecular dynamics simulations to explain how the membrane environment impacts the dual roles of CD59 in controlling pore formation of MAC, and as a target of bacterial virulence factors which hijack CD59 to lyse human cells.

Journal article

Yahiya S, Saunders CN, Hassan S, Straschil U, Fischer OJ, Rueda-Zubiaurre A, Haase S, Vizcay-Barrena G, Famodimu MT, Jordan S, Delves MJ, Tate EW, Barnard A, Fuchter MJ, Baum Jet al., 2023, A novel class of sulphonamides potently block malaria transmission by targeting a Plasmodium vacuole membrane protein, Disease Models &amp; Mechanisms, Vol: 16, Pages: 1-20, ISSN: 1754-8403

Phenotypic cell-based screens are critical tools for discovering candidate drugs for development, yet identification of the cellular target and mode of action of a candidate drug is often lacking. Using an imaging-based screen, we recently discovered an N-[(4-hydroxychroman-4-yl)methyl]-sulphonamide (N-4HCS) compound, DDD01035881, that blocks male gamete formation in the malaria parasite life cycle and subsequent transmission of the parasite to the mosquito with nanomolar activity. To identify the target(s) of DDD01035881, and of the N-4HCS class of compounds more broadly, we synthesised a photoactivatable derivative, probe 2. Photoaffinity labelling of probe 2 coupled with mass spectrometry identified the 16 kDa Plasmodium falciparum parasitophorous vacuole membrane protein Pfs16 as a potential parasite target. Complementary methods including cellular thermal shift assays confirmed that the parent molecule DDD01035881 stabilised Pfs16 in lysates from activated mature gametocytes. Combined with high-resolution, fluorescence and electron microscopy data, which demonstrated that parasites inhibited with N-4HCS compounds phenocopy the targeted deletion of Pfs16 in gametocytes, these data implicate Pfs16 as a likely target of DDD01035881. This finding establishes N-4HCS compounds as being flexible and effective starting candidates from which transmission-blocking antimalarials can be developed in the future.

Journal article

Fedoryshchak R, Gorelik A, Shen M, Shchepinova M, Pérez-Dorado I, Tate Eet al., 2023, Discovery of lipid-mediated protein–protein interactions in living cells using metabolic labeling with photoactivatable clickable probes, Chemical Science, Vol: 14, Pages: 2419-2430, ISSN: 2041-6520

Protein-protein interactions (PPIs) are essential and pervasive regulatory elements in cell biology. Despite development of a range of techniques to probe PPIs in living systems, there is a dearth of approaches to capture interactions driven by specific post-translational modifications (PTMs). Myristoylation is a lipid PTM added to more than 200 human proteins, where it may regulate membrane localization, stability or activity. Here we report design and synthesis of a panel of novel photocrosslinkable and clickable myristic acid analog probes, and their characterization as efficient substrates for human N -myristoyltransferases NMT1 and NMT2, both biochemically and through X-ray co-crystallography. We demonstrate metabolic incorporation of probes to label NMT substrates in cell culture and in situ intracellular photoactivation to form a covalent crosslink between modified proteins and their interactors, capturing a snapshot of interactions driven by the presence of the lipid PTM. Proteomic analyses revealed both known and multiple novel interactors of a series of myristoylated proteins, including ferroptosis suppressor protein FSP1 and spliceosome-associated RNA helicase DDX46. The concept exemplified by these probes offers an efficient approach for exploring the PTM-specific interactome, which may prove broadly applicable to other PTMs.

Journal article

Zhang L, Lovell S, De Vita E, Jagtap P, Lucy D, Goya Grocin A, Kjaer S, Borg A, Henning J, Miller A, Tate Eet al., 2022, A KLK6 activity-based probe reveals a role for KLK6 activity in pancreatic cancer cell invasion, Journal of the American Chemical Society, Vol: 144, Pages: 22493-22504, ISSN: 0002-7863

Pancreatic cancer has the lowest survival rate of all common cancers due to late diagnosis and limited treatment options. Serine hydrolases are known to mediate cancer progression and metastasis through initiation of signaling cascades and cleavage of extracellular matrix proteins, and the kallikrein-related peptidase (KLK) family of secreted serine proteases have emerging roles in pancreatic ductal adenocarcinoma (PDAC). However, the lack of reliable activity-based probes (ABPs) to profile KLK activity has hindered progress in validation of these enzymes as potential targets or biomarkers. Here, we developed potent and selective ABPs for KLK6 by using a positional scanning combinatorial substrate library and characterized their binding mode and interactions by X-ray crystallography. The optimized KLK6 probe IMP-2352 (kobs/I = 11,000 M–1 s–1) enabled selective detection of KLK6 activity in a variety of PDAC cell lines, and we observed that KLK6 inhibition reduced the invasiveness of PDAC cells that secrete active KLK6. KLK6 inhibitors were combined with N-terminomics to identify potential secreted protein substrates of KLK6 in PDAC cells, providing insights into KLK6-mediated invasion pathways. These novel KLK6 ABPs offer a toolset to validate KLK6 and associated signaling partners as targets or biomarkers across a range of diseases.

Journal article

Benns HJ, Storch M, Falco JA, Fisher FR, Tamaki F, Alves E, Wincott CJ, Milne R, Wiedemar N, Craven G, Baragaña B, Wyllie S, Baum J, Baldwin GS, Weerapana E, Tate EW, Child MAet al., 2022, CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery., Nat Microbiol

Nucleophilic amino acids are important in covalent drug development yet underutilized as anti-microbial targets. Chemoproteomic technologies have been developed to mine chemically accessible residues via their intrinsic reactivity towards electrophilic probes but cannot discern which chemically reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based oligo recombineering (CORe) platform to support the rapid identification, functional prioritization and rational targeting of chemically reactive sites in haploid systems. Our approach couples protein sequence and function with biological fitness of live cells. Here we profile the electrophile sensitivity of proteinogenic cysteines in the eukaryotic pathogen Toxoplasma gondii and prioritize functional sites using CORe. Electrophile-sensitive cysteines decorating the ribosome were found to be critical for parasite growth, with target-based screening identifying a parasite-selective anti-malarial lead molecule and validating the apicomplexan translation machinery as a target for ongoing covalent ligand development.

Journal article

Priyamvada L, Kallemeijn WW, Faronato M, Wilkins K, Goldsmith CS, Cotter CA, Ojeda S, Solari R, Moss B, Tate EW, Satheshkumar PSet al., 2022, Inhibition of vaccinia virus L1 N-myristoylation by the host N-myristoyltransferase inhibitor IMP-1088 generates non-infectious virions defective in cell entry, PLoS Pathogens, Vol: 18, ISSN: 1553-7366

We have recently shown that the replication of rhinovirus, poliovirus and foot-and-mouth disease virus requires the co-translational N-myristoylation of viral proteins by human host cell N-myristoyltransferases (NMTs), and is inhibited by treatment with IMP-1088, an ultrapotent small molecule NMT inhibitor. Here, we examine the importance of N-myristoylation during vaccinia virus (VACV) infection in primate cells and demonstrate the anti-poxviral effects of IMP-1088. N-myristoylated proteins from VACV and the host were metabolically labelled with myristic acid alkyne during infection using quantitative chemical proteomics. We identified VACV proteins A16, G9 and L1 to be N-myristoylated. Treatment with NMT inhibitor IMP-1088 potently abrogated VACV infection, while VACV gene expression, DNA replication, morphogenesis and EV formation remained unaffected. Importantly, we observed that loss of N-myristoylation resulted in greatly reduced infectivity of assembled mature virus particles, characterized by significantly reduced host cell entry and a decline in membrane fusion activity of progeny virus. While the N-myristoylation of VACV entry proteins L1, A16 and G9 was inhibited by IMP-1088, mutational and genetic studies demonstrated that the N-myristoylation of L1 was the most critical for VACV entry. Given the significant genetic identity between VACV, monkeypox virus and variola virus L1 homologs, our data provides a basis for further investigating the role of N-myristoylation in poxviral infections as well as the potential of selective NMT inhibitors like IMP-1088 as broad-spectrum poxvirus inhibitors.

Journal article

Zhang Q, Kounde C, Mondal M, Zhang L, Conole D, De Vita E, Fuchter M, Tate Eet al., 2022, Light-mediated multi-target protein degradation using arylazopyrazole photoswitchable PROTACs (AP-PROTACs), Chemical Communications, Vol: 58, Pages: 10933-10936, ISSN: 1359-7345

Light-activable spatiotemporal control of PROTAC-induced protein degradation was achieved with novel arylazopyrazole photoswitchable PROTACs (AP-PROTACs). The use of a promiscuous kinase inhibitor in the design enables this unique photoswitchable PROTAC to selectively degrade four protein kinases together with on/off optical control using different wavelengths of light.

Journal article

Jackson TR, Vuorinen A, Josa-Cullere L, Madden KS, Conole D, Cogswell TJ, Wilkinson IVL, Kettyle LM, Zhang D, O'Mahony A, Gracias D, McCall L, Westwood R, Terstappen GC, Davies SG, Tate EW, Wynne GM, Vyas P, Russell AJ, Milne TAet al., 2022, A tubulin binding molecule drives differentiation of acute myeloid leukemia cells, ISCIENCE, Vol: 25

Journal article

Ahmed A, Bickel JK, Andrei SA, Couves E, McAllister T, Kawamura A, Bubeck DA, Tate EWet al., 2022, Optimisation of Macrocyclic Peptide Hits Identified as CD59 Binders to Overcome Resistance in Cancer Immunotherapy, Publisher: WILEY, ISSN: 1075-2617

Conference paper

Priyamvada L, Kallemeijn WW, Faronato M, Wilkins K, Goldsmith CS, Cotter CA, Ojeda S, Solari R, Moss B, Tate EW, Satheshkumar PSet al., 2022, Inhibition of vaccinia virus L1 <i>N</i>-myristoylation by the host <i>N</i>-myristoyltransferase inhibitor IMP-1088 generates non-infectious virions defective in cell entry

<jats:title>ABSTRACT</jats:title><jats:p>We have recently shown that the replication of rhinovirus, poliovirus and foot-and-mouth disease virus requires the co-translational <jats:italic>N-</jats:italic>myristoylation of viral proteins by human host cell <jats:italic>N</jats:italic>-myristoyltransferases (NMTs), and is inhibited by treatment with IMP-1088, an ultrapotent small molecule NMT inhibitor. Here, we reveal the role of <jats:italic>N</jats:italic>-myristoylation during vaccinia virus (VACV) infection in human host cells and demonstrate the anti-poxviral effects of IMP-1088. <jats:italic>N-</jats:italic>myristoylated proteins from VACV and the host were metabolically labelled with myristic acid alkyne during infection using quantitative chemical proteomics. We identified VACV proteins A16, G9 and L1 to be <jats:italic>N-</jats:italic>myristoylated. Treatment with NMT inhibitor IMP-1088 potently abrogated VACV infection, while VACV gene expression, DNA replication, morphogenesis and EV formation remained unaffected. Importantly, we observed that loss of <jats:italic>N</jats:italic>-myristoylation resulted in greatly reduced infectivity of assembled mature virus particles, characterized by significantly reduced host cell entry and a decline in membrane fusion activity of progeny virus. While the <jats:italic>N</jats:italic>-myristoylation of VACV entry proteins L1, A16 and G9 was inhibited by IMP-1088, mutational and genetic studies demonstrated that the <jats:italic>N</jats:italic>-myristoylation of L1 was the most critical for VACV entry. Given the significant genetic identity between VACV, monkeypox virus and variola virus L1 homologs, our data provides a basis for further investigating the role of <jats:italic>N</jats:italic>-myristoylation in poxviral infections as well as the potential of selective NMT inhibitors like IMP-1088 as

Journal article

Williams D, Mahmoud M, Liu R, Andueza A, Kumar S, Kang D-W, Zhang J, Tamargo I, Villa-Roel N, Baek K-I, Lee H, An Y, Zhang L, Tate EW, Bagchi P, Pohl J, Mosnier LO, Diamandis EP, Mihara K, Hollenberg MD, Dai Z, Jo Het al., 2022, Stable flow-induced expression of KLK10 inhibits endothelial inflammation and atherosclerosis., eLife, Vol: 11, Pages: 1-23, ISSN: 2050-084X

Atherosclerosis preferentially occurs in arterial regions exposed to disturbed blood flow (d-flow), while regions exposed to stable flow (s-flow) are protected. The proatherogenic and atheroprotective effects of d-flow and s-flow are mediated in part by the global changes in endothelial cell gene expression, which regulates endothelial dysfunction, inflammation, and atherosclerosis. Previously, we identified Kallikrein-Related Peptidase 10 (Klk10, a secreted serine protease) as a flow-sensitive gene in mouse arterial endothelial cells, but its role in endothelial biology and atherosclerosis was unknown. Here, we show that KLK10 is upregulated under s-flow conditions and downregulated under d-flow conditions using in vivo& mouse models and in vitro studies with cultured endothelial cells (ECs). Single-cell RNA sequencing (scRNAseq) and scATAC sequencing (scATACseq) study using the partial carotid ligation mouse model showed flow-regulated Klk10 expression at the epigenomic and transcription levels. Functionally, KLK10 protected against d-flow-induced permeability dysfunction and inflammation in human artery ECs (HAECs), as determined by NFkB activation, expression of vascular cell adhesion molecule 1 (VCAM1) and intracellular adhesion molecule 1 (ICAM1), and monocyte adhesion. Further, treatment of mice in vivo with rKLK10 decreased arterial endothelial inflammation in d-flow regions. Additionally, rKLK10 injection or ultrasound-mediated transfection of Klk10-expressing plasmids inhibited atherosclerosis in Apoe-/- mice. Moreover, KLK10 expression was significantly reduced in human coronary arteries with advanced atherosclerotic plaques compared to those with less severe plaques. KLK10 is a flow-sensitive endothelial protein that serves as an anti-inflammatory, barrier-protective, and anti-atherogenic factor.

Journal article

Mondal M, Conole D, Nautiyal J, Tate Eet al., 2022, UCHL1 as a novel target in breast cancer: emerging insights from cell and chemical biology, British Journal of Cancer, Vol: 126, Pages: 24-33, ISSN: 0007-0920

Breast cancer has the highest incidence and death rate among cancers in women worldwide. In particular, metastatic Estrogen Receptor negative (ER–) breast cancer and Triple-Negative Breast Cancer (TNBC) subtypes have very limited treatment options, with low survival rates. Ubiquitin carboxyl terminal hydrolase L1 (UCHL1), a ubiquitin C-terminal hydrolase belonging to the deubiquitinase (DUB) family of enzymes, is highly expressed in these cancer types, and several key reports have revealed emerging and important roles for UCHL1 in breast cancer. However, selective and potent small molecule UCHL1 inhibitors have been disclosed only very recently, alongside chemical biology approaches to detect regulated UHCL1 activity in cancer cells. These tools will enable novel insights into oncogenic mechanisms driven by UCHL1, and identification of substrate proteins deubiquitinated by UCHL1, with the ultimate goal of realizing the potential of UCHL1 as a drug target in breast cancer.

Journal article

Andrei SA, Tate EW, Lanyon-Hogg T, 2022, Evaluating Hedgehog Acyltransferase Activity and Inhibition Using the Acylation-coupled Lipophilic Induction of Polarization (Acyl-cLIP) Assay., Methods Mol Biol, Vol: 2374, Pages: 13-26

Palmitoylation of the Hedgehog family of proteins is a critical step in the Hedgehog signaling pathway and is performed by the membrane-bound O-acyltransferase enzyme Hedgehog acyltransferase (HHAT). Measurement of HHAT activity has traditionally relied on radiolabeled fatty acid substrates, which imposes considerable constraints on throughput, cost, and safety, consequently hindering the efficient identification and development of small-molecule HHAT inhibitors. The Acylation-coupled Lipophilic Induction of Polarisation (Acyl-cLIP) assay was recently developed in our lab as a novel platform to evaluate lipidation of peptides in real time and high throughput. In this chapter, we describe the isolation of active HHAT from HEK293a cells and application of the Acyl-cLIP assay to characterize HHAT inhibitors. Our methodology uses standard chemical biology lab equipment and yields high-quality kinetic data from minimal sample volumes. The assay uses standard 384-well plates and is easily adapted to medium- or high-throughput screening formats.

Journal article

Jamshidiha M, Lanyon-Hogg T, Sutherell C, Craven G, Tersa M, De Vita E, Brustur D, Perez-Doraldo I, Hassan S, Petracca R, Morgan R, Sanz-Hernández M, Norman J, Armstrong A, Mann D, Cota E, Tate Eet al., 2021, Identification of the first structurally validated covalent ligands of the small GTPase RAB27A, RSC Medicinal Chemistry, Vol: 13, Pages: 150-155, ISSN: 2632-8682

Rab27A is a small GTPase, which mediates transport and docking of secretory vesicles at the plasma membrane via protein–protein interactions (PPIs) with effector proteins. Rab27A promotes the growth and invasion of multiple cancer types such as breast, lung and pancreatic, by enhancing secretion of chemokines, metalloproteases and exosomes. The significant role of Rab27A in multiple cancer types and the minor role in adults suggest that Rab27A may be a suitable target to disrupt cancer metastasis. Similar to many GTPases, the flat topology of the Rab27A-effector PPI interface and the high affinity for GTP make it a challenging target for inhibition by small molecules. Reported co-crystal structures show that several effectors of Rab27A interact with the Rab27A SF4 pocket (‘WF-binding pocket’) via a conserved tryptophan–phenylalanine (WF) dipeptide motif. To obtain structural insight into the ligandability of this pocket, a novel construct was designed fusing Rab27A to part of an effector protein (fRab27A), allowing crystallisation of Rab27A in high throughput. The paradigm of KRas covalent inhibitor development highlights the challenge presented by GTPase proteins as targets. However, taking advantage of two cysteine residues, C123 and C188, that flank the WF pocket and are unique to Rab27A and Rab27B among the >60 Rab family proteins, we used the quantitative Irreversible Tethering (qIT) assay to identify the first covalent ligands for native Rab27A. The binding modes of two hits were elucidated by co-crystallisation with fRab27A, exemplifying a platform for identifying suitable lead fragments for future development of competitive inhibitors of the Rab27A-effector interaction interface, corroborating the use of covalent libraries to tackle challenging targets.

Journal article

Coupland CE, Andrei SA, Ansell TB, Carrique L, Kumar P, Sefer L, Schwab RA, Byrne EFX, Pardon E, Steyaert J, Magee A, Lanyon-Hogg T, Sansom MSP, Tate EW, Siebold Cet al., 2021, Structure, mechanism, and inhibition of Hedgehog acyltransferase, Molecular Cell, Vol: 81, Pages: 5025-+, ISSN: 1097-2765

The Sonic Hedgehog (SHH) morphogen pathway is fundamental for embryonic development and stem cell maintenance and is implicated in various cancers. A key step in signaling is transfer of a palmitate group to the SHH N terminus, catalyzed by the multi-pass transmembrane enzyme Hedgehog acyltransferase (HHAT). We present the high-resolution cryo-EM structure of HHAT bound to substrate analog palmityl-coenzyme A and a SHH-mimetic megabody, revealing a heme group bound to HHAT that is essential for HHAT function. A structure of HHAT bound to potent small-molecule inhibitor IMP-1575 revealed conformational changes in the active site that occlude substrate binding. Our multidisciplinary analysis provides a detailed view of the mechanism by which HHAT adapts the membrane environment to transfer an acyl chain across the endoplasmic reticulum membrane. This structure of a membrane-bound O-acyltransferase (MBOAT) superfamily member provides a blueprint for other protein-substrate MBOATs and a template for future drug discovery.

Journal article

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