Search Results

You searched for all publications:

with publication states 'Published (Approved)'

Search Again...

These results only include publications that have been reviewed and processed by Diamond Light Source. To also view papers that have not yet been processed click here.

You can use the folder icon under Actions to collate papers as required. You can then click on View Folder in the left-hand navigation to review and/or download your folder.

Exact matches
Related results

52 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4, 5, 6 [Next/Last]

Instruments / Technical Area	Publication Details	Published
I04-Macromolecular Crystallography	Exploring the interaction of N-(benzothiazol-2-yl)pyrrolamide DNA gyrase inhibitors with the GyrB ATP-binding site lipophilic floor: A medicinal chemistry and QTAIM study Nace Zidar , Andrej Emanuel Cotman , Wessel Sinnige , Ondrej Benek , Michaela Barančokova , Anamarija Zega , Lucija Peterlin Mašič , Tihomir Tomašič , Janez Ilaš , Sara R. Henderson , Julia E. A. Mundy , Anthony Maxwell , Clare E. M. Stevenson , David M. Lawson , Geert Jan Sterk , Rodrigo Tosso , Lucas Gutierrez , Ricardo D. Enriz , Danijel Kikelj Bioorganic & Medicinal Chemistry 43 DOI: 10.1016/j.bmc.2024.117798 Diamond Proposal Number(s): [18565] Open Access Show Abstract ▼ Abstract: N-(Benzothiazole-2-yl)pyrrolamide DNA gyrase inhibitors with benzyl or phenethyl substituents attached to position 3 of the benzothiazole ring or to the carboxamide nitrogen atom were prepared and studied for their inhibition of Escherichia coli DNA gyrase by supercoiling assay. Compared to inhibitors bearing the substituents at position 4 of the benzothiazole ring, the inhibition was attenuated by moving the substituent to position 3 and further to the carboxamide nitrogen atom. A co-crystal structure of (Z)-3-benzyl-2-((4,5-dibromo-1H-pyrrole-2-carbonyl)imino)-2,3-dihydrobenzo[d]-thiazole-6-carboxylic acid (I) in complex with E. coli GyrB24 (ATPase subdomain) was solved, revealing the binding mode of this type of inhibitor to the ATP-binding pocket of the E. coli GyrB subunit. The key binding interactions were identified and their contribution to binding was rationalised by quantum theory of atoms in molecules (QTAIM) analysis. Our study shows that the benzyl or phenethyl substituents bound to the benzothiazole core interact with the lipophilic floor of the active site, which consists mainly of residues Gly101, Gly102, Lys103 and Ser108. Compounds with substituents at position 3 of the benzothiazole core were up to two orders of magnitude more effective than compounds with substituents at the carboxamide nitrogen. In addition, the 6-oxalylamino compounds were more potent inhibitors of E. coli DNA gyrase than the corresponding 6-acetamido analogues.	Jun 2024
I04-Macromolecular Crystallography	Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation Qun Liu , Abbas Maqbool , Federico G. Mirkin , Yeshveer Singh , Clare E. M. Stevenson , David M. Lawson , Sophien Kamoun , Weijie Huang , Saskia A. Hogenhout Proceedings Of The National Academy Of Sciences 120 DOI: 10.1073/pnas.2310664120 Diamond Proposal Number(s): [25108] Open Access Show Abstract ▼ Abstract: In eukaryotes, targeted protein degradation (TPD) typically depends on a series of interactions among ubiquitin ligases that transfer ubiquitin molecules to substrates leading to degradation by the 26S proteasome. We previously identified that the bacterial effector protein SAP05 mediates ubiquitin-independent TPD. SAP05 forms a ternary complex via interactions with the von Willebrand Factor Type A (vWA) domain of the proteasomal ubiquitin receptor Rpn10 and the zinc-finger (ZnF) domains of the SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) and GATA BINDING FACTOR (GATA) transcription factors (TFs). This leads to direct TPD of the TFs by the 26S proteasome. Here, we report the crystal structures of the SAP05–Rpn10vWA complex at 2.17 Å resolution and of the SAP05–SPL5ZnF complex at 2.20 Å resolution. Structural analyses revealed that SAP05 displays a remarkable bimodular architecture with two distinct nonoverlapping surfaces, a “loop surface” with three protruding loops that form electrostatic interactions with ZnF, and a “sheet surface” featuring two β-sheets, loops, and α-helices that establish polar interactions with vWA. SAP05 binding to ZnF TFs involves single amino acids responsible for multiple contacts, while SAP05 binding to vWA is more stable due to the necessity of multiple mutations to break the interaction. In addition, positioning of the SAP05 complex on the 26S proteasome points to a mechanism of protein degradation. Collectively, our findings demonstrate how a small bacterial bimodular protein can bypass the canonical ubiquitin–proteasome proteolysis pathway, enabling ubiquitin-independent TPD in eukaryotic cells. This knowledge holds significant potential for the creation of TPD technologies.	Dec 2023
I04-Macromolecular Crystallography	Allelic compatibility in plant immune receptors facilitates engineering of new effector recognition specificities Adam R. Bentham , Juan Carlos De La Concepcion , Javier Vega Benjumea , Jiorgos Kourelis , Sally Jones , Melanie Mendel , Jack Stubbs , Clare E. M. Stevenson , Josephine H. R. Maidment , Mark Youles , Rafal Zdrzalek , Sophien Kamoun , Mark J. Banfield The Plant Cell DOI: 10.1093/plcell/koad204 Diamond Proposal Number(s): [25108] Open Access Show Abstract ▼ Abstract: Engineering the plant immune system offers genetic solutions to mitigate crop diseases caused by diverse agriculturally significant pathogens and pests. Modification of intracellular plant immune receptors of the nucleotide-binding leucine rich repeat (NLR) superfamily for expanded recognition of pathogen virulence proteins (effectors) is a promising approach for engineering disease resistance. However, engineering can cause NLR autoactivation, resulting in constitutive defence responses that are deleterious to the plant. This may be due to plant NLRs associating in highly complex signalling networks that co-evolve together, and changes through breeding or genetic modification can generate incompatible combinations, resulting in autoimmune phenotypes. The sensor and helper NLRs of the rice (Oryza sativa) NLR pair Pik have co-evolved, and mismatching between non-co-evolved alleles triggers constitutive activation and cell death. This limits the extent to which protein modifications can be used to engineer pathogen recognition and enhance disease resistance mediated by these NLRs. Here, we dissected incompatibility determinants in the Pik pair in Nicotiana benthamiana and found that heavy metal-associated (HMA) domains integrated in Pik-1 not only evolved to bind pathogen effectors but also likely co-evolved with other NLR domains to maintain immune homeostasis. This explains why changes in integrated domains can lead to autoactivation. We then used this knowledge to facilitate engineering of new effector recognition specificities, overcoming initial autoimmune penalties. We show that by mismatching alleles of the rice sensor and helper NLRs Pik-1 and Pik-2, we can enable the integration of synthetic domains with novel and enhanced recognition specificities. Taken together, our results reveal a strategy for engineering NLRs, which has the potential to allow an expanded set of integrations and therefore new disease resistance specificities in plants.	Jul 2023
I03-Macromolecular Crystallography	Exploring the 5-substituted 2-aminobenzothiazole-based DNA Gyrase B inhibitors active against ESKAPE pathogens Maša Sterle , Martina Durcik , Clare E. M. Stevenson , Sara Henderson , Petra Eva Szili , Marton Czikkely , David M. Lawson , Anthony Maxwell , Dominique Cahard , Danijel Kikelj , Nace Zidar , Csaba Pal , Lucija Peterlin Mašič , Janez Ilaš , Tihomir Tomašič , Andrej Emanuel Cotman , Anamarija Zega Acs Omega DOI: 10.1021/acsomega.3c01930 Diamond Proposal Number(s): [18565] Open Access Show Abstract ▼ Abstract: We present a new series of 2-aminobenzothiazole-based DNA gyrase B inhibitors with promising activity against ESKAPE bacterial pathogens. Based on the binding information extracted from the cocrystal structure of DNA gyrase B inhibitor A, in complex with Escherichia coli GyrB24, we expanded the chemical space of the benzothiazole-based series to the C5 position of the benzothiazole ring. In particular, compound E showed low nanomolar inhibition of DNA gyrase (IC50 < 10 nM) and broad-spectrum antibacterial activity against pathogens belonging to the ESKAPE group, with the minimum inhibitory concentration < 0.03 μg/mL for most Gram-positive strains and 4–16 μg/mL against Gram-negative E. coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae. To understand the binding mode of the synthesized inhibitors, a combination of docking calculations, molecular dynamics (MD) simulations, and MD-derived structure-based pharmacophore modeling was performed. The computational analysis has revealed that the substitution at position C5 can be used to modify the physicochemical properties and antibacterial spectrum and enhance the inhibitory potency of the compounds. Additionally, a discussion of challenges associated with the synthesis of 5-substituted 2-aminobenzothiazoles is presented.	Jun 2023
I03-Macromolecular Crystallography	Resurrection of plant disease resistance proteins via helper NLR bioengineering Mauricio P. Contreras , Hsuan Pai , Muniyandi Selvaraj , Amirali Toghani , David M. Lawson , Yasin Tumtas , Cian Duggan , Enoch Lok Him Yuen , Clare E. M. Stevenson , Adeline Harant , Abbas Maqbool , Chih-Hang Wu , Tolga O. Bozkurt , Sophien Kamoun , Lida Derevnina Science Advances 9 DOI: 10.1126/sciadv.adg3861 Diamond Proposal Number(s): [18565] Open Access Show Abstract ▼ Abstract: Parasites counteract host immunity by suppressing helper nucleotide binding and leucine-rich repeat (NLR) proteins that function as central nodes in immune receptor networks. Understanding the mechanisms of immunosuppression can lead to strategies for bioengineering disease resistance. Here, we show that a cyst nematode virulence effector binds and inhibits oligomerization of the helper NLR protein NRC2 by physically preventing intramolecular rearrangements required for activation. An amino acid polymorphism at the binding interface between NRC2 and the inhibitor is sufficient for this helper NLR to evade immune suppression, thereby restoring the activity of multiple disease resistance genes. This points to a potential strategy for resurrecting disease resistance in crop genomes.	May 2023
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Effector target-guided engineering of an integrated domain expands the disease resistance profile of a rice NLR immune receptor Josephine H. R. Maidment , Motoki Shimizu , Adam R. Bentham , Sham Vera , Marina Franceschetti , Apinya Longya , Clare E. M. Stevenson , Juan Carlos De La Concepcion , Aleksandra Bialas , Sophien Kamoun , Ryohei Terauchi , Mark J. Banfield Elife 12 DOI: 10.7554/eLife.81123 Diamond Proposal Number(s): [13467, 18565] Open Access Show Abstract ▼ Abstract: A subset of plant intracellular NLR immune receptors detect effector proteins, secreted by phytopathogens to promote infection, through unconventional integrated domains which resemble the effector’s host targets. Direct binding of effectors to these integrated domains activates plant defenses. The rice NLR receptor Pik-1 binds the Magnaporthe oryzae effector AVR-Pik through an integrated heavy metal-associated (HMA) domain. However, the stealthy alleles AVR-PikC and AVR-PikF avoid interaction with Pik-HMA and evade host defenses. Here, we exploited knowledge of the biochemical interactions between AVR-Pik and its host target, OsHIPP19, to engineer novel Pik-1 variants that respond to AVR-PikC/F. First, we exchanged the HMA domain of Pikp-1 for OsHIPP19-HMA, demonstrating that effector targets can be incorporated into NLR receptors to provide novel recognition profiles. Second, we used the structure of OsHIPP19-HMA to guide the mutagenesis of Pikp-HMA to expand its recognition profile. We demonstrate that the extended recognition profiles of engineered Pikp-1 variants correlate with effector binding in planta and in vitro, and with the gain of new contacts across the effector/HMA interface. Crucially, transgenic rice producing the engineered Pikp-1 variants was resistant to blast fungus isolates carrying AVR-PikC or AVR-PikF. These results demonstrate that effector target-guided engineering of NLR receptors can provide new-to-nature disease resistance in crops.	May 2023
I04-Macromolecular Crystallography	New dual inhibitors of bacterial topoisomerases with broad-spectrum antibacterial activity and in vivo efficacy against vancomycin-intermediate Staphylococcus aureus Martina Durcik , Andrej Emanuel Cotman , Žan Toplak , Štefan Možina , Žiga Skok , Petra Eva Szili , Márton Czikkely , Elvin Maharramov , Thu Hien Vu , Maria Vittoria Piras , Nace Zidar , Janez Ilaš , Anamarija Zega , Jurij Trontelj , Luis A. Pardo , Diarmaid Hughes , Douglas Huseby , Tália Berruga-Fernández , Sha Cao , Ivailo Simoff , Richard Svensson , Sergiy V. Korol , Zhe Jin , Francisca Vicente , Maria C. Ramos , Julia E. A. Mundy , Anthony Maxwell , Clare E. M. Stevenson , David M. Lawson , Björn Glinghammar , Eva Sjöström , Martin Bohlin , Joanna Oreskär , Sofie Alvér , Guido V. Janssen , Geert Jan Sterk , Danijel Kikelj , Csaba Pal , Tihomir Tomašič , Lucija Peterlin Mašič Journal Of Medicinal Chemistry 1703 DOI: 10.1021/acs.jmedchem.2c01905 Diamond Proposal Number(s): [25108] Open Access Show Abstract ▼ Abstract: A new series of dual low nanomolar benzothiazole inhibitors of bacterial DNA gyrase and topoisomerase IV were developed. The resulting compounds show excellent broad-spectrum antibacterial activities against Gram-positive Enterococcus faecalis, Enterococcus faecium and multidrug resistant (MDR) Staphylococcus aureus strains [best compound minimal inhibitory concentrations (MICs): range, <0.03125–0.25 μg/mL] and against the Gram-negatives Acinetobacter baumannii and Klebsiella pneumoniae (best compound MICs: range, 1–4 μg/mL). Lead compound 7a was identified with favorable solubility and plasma protein binding, good metabolic stability, selectivity for bacterial topoisomerases, and no toxicity issues. The crystal structure of 7a in complex with Pseudomonas aeruginosa GyrB24 revealed its binding mode at the ATP-binding site. Expanded profiling of 7a and 7h showed potent antibacterial activity against over 100 MDR and non-MDR strains of A. baumannii and several other Gram-positive and Gram-negative strains. Ultimately, in vivo efficacy of 7a in a mouse model of vancomycin-intermediate S. aureus thigh infection was also demonstrated.	Mar 2023
I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Discovery and hit-to-lead optimization of benzothiazole scaffold-based DNA gyrase inhibitors with potent activity against Acinetobacter baumannii and Pseudomonas aeruginosa Andrej Emanuel Cotman , Martina Durcik , Davide Benedetto Tiz , Federica Fulgheri , Daniela Secci , Maša Sterle , Štefan Možina , Žiga Skok , Nace Zidar , Anamarija Zega , Janez Ilaš , Lucija Peterlin Mašič , Tihomir Tomašič , Diarmaid Hughes , Douglas L. Huseby , Sha Cao , Linnéa Garoff , Talía Berruga Fernández , Paraskevi Giachou , Lisa Crone , Ivailo Simoff , Richard Svensson , Bryndis Birnir , Sergiy V. Korol , Zhe Jin , Francisca Vicente , Maria C. Ramos , Mercedes De La Cruz , Björn Glinghammar , Lena Lenhammar , Sara R. Henderson , Julia E. A. Mundy , Anthony Maxwell , Claren E. M. Stevenson , David M. Lawson , Guido V. Janssen , Geert Jan Sterk , Danijel Kikelj Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.2c01597 Diamond Proposal Number(s): [18565, 25108] Open Access Show Abstract ▼ Abstract: We have developed compounds with a promising activity against Acinetobacter baumannii and Pseudomonas aeruginosa, which are both on the WHO priority list of antibiotic-resistant bacteria. Starting from DNA gyrase inhibitor 1, we identified compound 27, featuring a 10-fold improved aqueous solubility, a 10-fold improved inhibition of topoisomerase IV from A. baumannii and P. aeruginosa, a 10-fold decreased inhibition of human topoisomerase IIα, and no cross-resistance to novobiocin. Cocrystal structures of 1 in complex with Escherichia coli GyrB24 and (S)-27 in complex with A. baumannii GyrB23 and P. aeruginosa GyrB24 revealed their binding to the ATP-binding pocket of the GyrB subunit. In further optimization steps, solubility, plasma free fraction, and other ADME properties of 27 were improved by fine-tuning of lipophilicity. In particular, analogs of 27 with retained anti-Gram-negative activity and improved plasma free fraction were identified. The series was found to be nongenotoxic, nonmutagenic, devoid of mitochondrial toxicity, and possessed no ion channel liabilities.	Jan 2023
I03-Macromolecular Crystallography	Expansion of the catalytic repertoire of alcohol dehydrogenases in plant metabolism Chloe Langley , Evangelos Tatsis , Benke Hong , Yoko Nakamura , Christian Paetz , Clare E. M. Stevenson , Jerome Basquin , David M. Lawson , Lorenzo Caputi , Sarah E. O'Connor Angewandte Chemie International Edition DOI: 10.1002/anie.202210934 Diamond Proposal Number(s): [13467] Open Access Show Abstract ▼ Abstract: Medium-chain alcohol dehydrogenases (ADHs) comprise a highly conserved enzyme family that catalyse the reversible reduction of aldehydes. However, recent discoveries in plant natural product biosynthesis suggest that the catalytic repertoire of ADHs has been expanded. Here we report the crystal structure of dihydroprecondylocarpine acetate synthase (DPAS), an ADH that catalyses the non-canonical 1,4-reduction of an α,β -unsaturated iminium moiety. Comparison with structures of plant-derived ADHs suggest the 1,4-iminium reduction does not require a proton relay or the presence of a catalytic zinc ion in contrast to canonical 1,2-aldehyde reducing ADHs that require the catalytic zinc and a proton relay. Furthermore, ADHs that catalysed 1,2-iminium reduction required the presence of the catalytic zinc and the loss of the proton relay. This suggests how the ADH active site can be modified to perform atypical carbonyl reductions, providing insight into how chemical reactions are diversified in plant metabolism.	Oct 2022
I03-Macromolecular Crystallography	Structural insights into the mechanism of adaptive ribosomal modification by Pseudomonas RimK Catriona M. A. Thompson , Richard H. Little , Clare E. M. Stevenson , David M. Lawson , Jacob G. Malone Proteins: Structure, Function, And Bioinformatics DOI: 10.1002/prot.26429 Diamond Proposal Number(s): [13467] Open Access Show Abstract ▼ Abstract: Bacteria are equipped with a diverse set of regulatory tools that allow them to quickly adapt to their environment. The RimK system allows for Pseudomonas spp. to adapt through post-transcriptional regulation by altering the ribosomal subunit RpsF. RimK is found in a wide range of bacteria with a conserved amino acid sequence, however the genetic context and the role of this protein is highly diverse. By solving and comparing the structures of RimK homologues from two related but functionally divergent systems, we uncovered key structural differences that likely contribute to the different activity levels of each of these homologues. Moreover, we were able to clearly resolve the active site of this protein for the first time, resolving binding of the glutamate substrate. This work advances our understanding of how subtle differences in protein sequence and structure can have profound effects on protein activity, which can in turn result in widespread mechanistic changes.	Sep 2022

Publications Database

Search Results

You searched for all publications:

Search Again...

Subject Areas (check all that apply) select all

Instruments used to collect data (check all that apply) select all

Collaborations involved (check all that apply) select all

Diamond Offline Facilities used

Relevant Technical Areas (check all that apply) select all

Menu for Anonymous User