I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Timothy P. C.
Rooney
,
Panagis
Filippakopoulos
,
Oleg
Fedorov
,
Sarah
Picaud
,
Wilian A.
Cortopassi
,
Duncan A.
Hay
,
Sarah
Martin
,
Anthony
Tumber
,
Catherine M.
Rogers
,
Martin
Philpott
,
Minghua
Wang
,
Amber L.
Thompson
,
Tom D.
Heightman
,
David C.
Pryde
,
Andrew
Cook
,
Robert S.
Paton
,
Susanne
Müller
,
Stefan
Knapp
,
Paul E.
Brennan
,
Stuart J.
Conway
Diamond Proposal Number(s):
[8421]
Open Access
Abstract: The benzoxazinone and dihydroquinoxalinone fragments were employed as novel acetyl lysine mimics in the development of CREBBP bromodomain ligands. While the benzoxazinone series showed low affinity for the CREBBP bromodomain, expansion of the dihydroquinoxalinone series resulted in the first potent inhibitors of a bromodomain outside the BET family. Structural and computational studies reveal that an internal hydrogen bond stabilizes the protein-bound conformation of the dihydroquinoxalinone series. The side chain of this series binds in an induced-fit pocket forming a cation–? interaction with R1173 of CREBBP. The most potent compound inhibits binding of CREBBP to chromatin in U2OS cells.
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Jun 2014
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I04-Macromolecular Crystallography
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Raquel C.
Montenegro
,
Peter G. K.
Clark
,
Alison
Howarth
,
Xiao
Wan
,
Alessandro
Ceroni
,
Paulina
Siejka
,
Graciela A.
Nunez-Alonso
,
Octovia
Monteiro
,
Catherine
Rogers
,
Vicki
Gamble
,
Rommel
Burbano
,
Paul E.
Brennan
,
Cynthia
Tallant
,
Daniel
Ebner
,
Oleg
Fedorov
,
Eric
O'Neill
,
Stefan
Knapp
,
Darren
Dixon
,
Susanne
Müller
Diamond Proposal Number(s):
[10619]
Open Access
Abstract: Gastric cancer is one of the most common malignancies and a leading cause of cancer death worldwide. The prognosis of stomach cancer is generally poor as this cancer is not very sensitive to commonly used chemotherapies. Epigenetic modifications play a key role in gastric cancer and contribute to the development and progression of this malignancy. In order to explore new treatment options in this target area we have screened a library of epigenetic inhibitors against gastric cancer cell lines and identified inhibitors for the BET family of bromodomains as potent inhibitors of gastric cancer cell proliferations. Here we show that both the pan-BET inhibitor (+)-JQ1 as well as a newly developed specific isoxazole inhibitor, PNZ5, showed potent inhibition of gastric cancer cell growth. Intriguingly, we found differences in the antiproliferative response between gastric cancer cells tested derived from Brazilian patients as compared to those from Asian patients, the latter being largely resistant to BET inhibition. As BET inhibitors are entering clinical trials these findings provide the first starting point for future therapies targeting gastric cancer.
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Nov 2014
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I02-Macromolecular Crystallography
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Léa
Bouché
,
Clara D.
Christ
,
Stephan
Siegel
,
Amaury E.
Fernández-Montalván
,
Simon J.
Holton
,
Oleg
Fedorov
,
Antonius
Ter Laak
,
Tatsuo
Sugawara
,
Detlef
Stöckigt
,
Cynthia
Tallant
,
James
Bennett
,
Octovia
Monteiro
,
Laura
Díaz-Sáez
,
Paulina
Siejka
,
Julia
Meier
,
Vera
Pütter
,
Jörg
Weiske
,
Susanne
Müller
,
Kilian V. M.
Huber
,
Ingo V.
Hartung
,
Bernard
Haendler
Diamond Proposal Number(s):
[15558, 10619]
Abstract: Bromodomains (BD) are readers of lysine acetylation marks present in numerous proteins associated with chromatin. Here we describe a dual inhibitor of the bromodomain and PHD finger (BRPF) family member BRPF2 and the TATA box binding protein-associated factors TAF1 and TAF1L. These proteins are found in large chromatin complexes and play important roles in transcription regulation. The substituted benzoisoquinolinedione series was identified by high-throughput screening, and subsequent structure–activity relationship optimization allowed generation of low nanomolar BRPF2 BD inhibitors with strong selectivity against BRPF1 and BRPF3 BDs. In addition, a strong inhibition of TAF1/TAF1L BD2 was measured for most derivatives. The best compound of the series was BAY-299, which is a very potent, dual inhibitor with an IC50 of 67 nM for BRPF2 BD, 8 nM for TAF1 BD2, and 106 nM for TAF1L BD2. Importantly, no activity was measured for BRD4 BDs. Furthermore, cellular activity was evidenced using a BRPF2– or TAF1–histone H3.3 or H4 interaction assay.
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May 2017
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
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Ariane
Hammitzsch
,
Cynthia
Tallant Blanco
,
Oleg
Fedorov
,
Alison
O’mahony
,
Paul E.
Brennan
,
Duncan A.
Hay
,
Fernando O.
Martinez
,
M. Hussein
Al-Mossawi
,
Jelle
De Wit
,
Matteo
Vecellio
,
Christopher
Wells
,
Paul
Wordsworth
,
Susanne
Müller
,
Stefan
Knapp
,
Paul
Bowness
Diamond Proposal Number(s):
[8421]
Abstract: Th17 responses are critical to a variety of human autoimmune diseases, and therapeutic targeting with monoclonal antibodies against IL-17 and IL-23 has shown considerable promise. Here, we report data to support selective bromodomain blockade of the transcriptional coactivators CBP (CREB binding protein) and p300 as an alternative approach to inhibit human Th17 responses. We show that CBP30 has marked molecular specificity for the bromodomains of CBP and p300, compared with 43 other bromodomains. In unbiased cellular testing on a diverse panel of cultured primary human cells, CBP30 reduced immune cell production of IL-17A and other proinflammatory cytokines. CBP30 also inhibited IL-17A secretion by Th17 cells from healthy donors and patients with ankylosing spondylitis and psoriatic arthritis. Transcriptional profiling of human T cells after CBP30 treatment showed a much more restricted effect on gene expression than that observed with the pan-BET (bromo and extraterminal domain protein family) bromodomain inhibitor JQ1. This selective targeting of the CBP/p300 bromodomain by CBP30 will potentially lead to fewer side effects than with the broadly acting epigenetic inhibitors currently in clinical trials.
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Aug 2015
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I02-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Niall
Igoe
,
Elliott D.
Bayle
,
Oleg
Fedorov
,
Cynthia
Tallant
,
Pavel
Savitsky
,
Catherine
Rogers
,
Dafydd R.
Owen
,
Gauri
Deb
,
Tim C. P.
Somervaille
,
David M.
Andrews
,
Neil
Jones
,
Anne
Cheasty
,
Hamish
Ryder
,
Paul E.
Brennan
,
Susanne
Müller
,
Stefan
Knapp
,
Paul V.
Fish
Abstract: The BRPF (bromodomain and PHD finger-containing) family are scaffolding proteins important for the recruitment of histone acetyltransferases of the MYST family to chromatin. Evaluation of the BRPF family as a potential drug target is at an early stage although there is an emerging understanding of a role in acute myeloid leukemia (AML). We report the optimization of fragment hit 5b to 13-d as a biased, potent inhibitor of the BRD of the BRPFs with excellent selectivity over nonclass IV BRD proteins. Evaluation of 13-d in a panel of cancer cell lines showed a selective inhibition of proliferation of a subset of AML lines. Pharmacokinetic studies established that 13-d had properties compatible with oral dosing in mouse models of disease (Fpo 49%). We propose that NI-42 (13-d) is a new chemical probe for the BRPFs suitable for cellular and in vivo studies to explore the fundamental biology of these proteins.
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Jan 2017
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I03-Macromolecular Crystallography
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Niall
Igoe
,
Elliott D.
Bayle
,
Cynthia
Tallant
,
Oleg
Fedorov
,
Julia C.
Meier
,
Pavel
Savitsky
,
Catherine
Rogers
,
Yannick
Morias
,
Sarah
Scholze
,
Helen
Boyd
,
Danen
Cunoosamy
,
David M.
Andrews
,
Anne
Cheasty
,
Paul E.
Brennan
,
Susanne
Müller
,
Stefan
Knapp
,
Paul V.
Fish
Abstract: The bromodomain and plant homeodomain finger-containing (BRPF) family are scaffolding proteins important for the recruitment of histone acetyltransferases of the MYST family to chromatin. Here, we describe NI-57 (16) as new pan-BRPF chemical probe of the bromodomain (BRD) of the BRPFs. Inhibitor 16 preferentially bound the BRD of BRPF1 and BRPF2 over BRPF3, whereas binding to BRD9 was weaker. Compound 16 has excellent selectivity over nonclass IV BRD proteins. Target engagement of BRPF1B and BRPF2 with 16 was demonstrated in nanoBRET and FRAP assays. The binding of 16 to BRPF1B was rationalized through an X-ray cocrystal structure determination, which showed a flipped binding orientation when compared to previous structures. We report studies that show 16 has functional activity in cellular assays by modulation of the phenotype at low micromolar concentrations in both cancer and inflammatory models. Pharmacokinetic data for 16 was generated in mouse with single dose administration showing favorable oral bioavailability.
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Jul 2017
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I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Sandra
Röhm
,
Benedict-Tilman
Berger
,
Martin
Schröder
,
Deep
Chatterjee
,
Sebastian
Mathea
,
Andreas C.
Joerger
,
Daniel M.
Pinkas
,
Joshua C.
Bufton
,
Amelie
Tjaden
,
Lohitesh
Kovooru
,
Mark
Kudolo
,
Christian
Pohl
,
Alex N.
Bullock
,
Susanne
Müller
,
Stefan
Laufer
,
Stefan
Knapp
Abstract: Discoidin domain receptors 1 and 2 (DDR1/2) play a central role in fibrotic disorders, such as renal and pulmonary fibrosis, atherosclerosis, and various forms of cancer. Potent and selective inhibitors, so-called chemical probe compounds, have been developed to study DDR1/2 kinase signaling. However, these inhibitors showed undesired activity on other kinases such as the tyrosine protein kinase receptor TIE or tropomyosin receptor kinases, which are related to angiogenesis and neuronal toxicity. In this study, we optimized our recently published p38 mitogen-activated protein kinase inhibitor 7 toward a potent and cell-active dual DDR/p38 chemical probe and developed a structurally related negative control. The structure-guided design approach used provided insights into the P-loop folding process of p38 and how targeting of non-conserved amino acids modulates inhibitor selectivity. The developed and comprehensively characterized DDR/p38 probe, 30 (SR-302), is a valuable tool for studying the role of DDR kinase in normal physiology and in disease development.
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Sep 2021
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I04-Macromolecular Crystallography
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Abstract: CBP (CREB (cAMP responsive element binding protein) binding protein (CREBBP)) and P300 (adenovirus E1A-associated 300 kDa protein) are two closely related histone acetyltransferases (HATs) that play a key role in the regulation of gene transcription. Both proteins contain a bromodomain flanking the HAT catalytic domain that is important for the targeting of CBP/P300 to chromatin and which offeres an opportunity for the development of protein–protein interaction inhibitors. Here we present the development of CBP/P300 bromodomain inhibitors with 2,3,4,5-tetrahydro-1,4-benzoxazepine backbone, an N-acetyl-lysine mimetic scaffold that led to the recent development of the chemical probe I-CBP112. We present comprehensive SAR of this inhibitor class as well as demonstration of cellular on target activity of the most potent and selective inhibitor TPOP146, which showed 134 nM affinity for CBP with excellent selectivity over other bromodomains.
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Oct 2016
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I03-Macromolecular Crystallography
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Michael
Forster
,
Apirat
Chaikuad
,
Teodor
Dimitrov
,
Eva
Döring
,
Julia
Holstein
,
Benedict-Tilman
Berger
,
Matthias
Gehringer
,
Kamran
Ghoreschi
,
Susanne
Müller
,
Stefan
Knapp
,
Stefan A.
Laufer
Diamond Proposal Number(s):
[10619]
Abstract: Janus kinases are major drivers of immune signaling and have been the focus of anti-inflammatory drug discovery for more than a decade. Because of the invariable co-localization of JAK1 and JAK3 at cytokine receptors, the question if selective JAK3 inhibition is sufficient to effectively block downstream signaling has been highly controversial. Recently, we discovered the covalent-reversible JAK3 inhibitor FM-381 (23) featuring high isoform and kinome selectivity. Crystallography revealed that this inhibitor induces an unprecedented binding pocket by interactions of a nitrile substituent with arginine residues in JAK3. Herein we describe detailed structure activity relationships necessary for induction of the arginine pocket and the impact of this structural change on potency, isoform selectivity and efficacy in cellular models. Furthermore, we evaluated the stability of this novel inhibitor class in in vitro metabolic assays and were able to demonstrate an adequate stability of key compound 23 for in vivo use.
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May 2018
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Vassilios
Myrianthopoulos
,
Nicolas
Gaboriaud-Kolar
,
Cynthia
Tallant
,
Michelle-Lynn
Hall
,
Stylianos
Grigoriou
,
Peter Moore
Brownlee
,
Oleg
Fedorov
,
Catherine
Rogers
,
David
Heidenreich
,
Marek
Wanior
,
Nikolaos
Drosos
,
Nikitia
Mexia
,
Pavel
Savitsky
,
Tina
Bagratuni
,
Efstathios
Kastritis
,
Evangelos
Terpos
,
Panagis
Filippakopoulos
,
Susanne
Müller
,
Alexios-Leandros
Skaltsounis
,
Jessica Ann
Downs
,
Stefan
Knapp
,
Emmanuel
Mikros
Open Access
Abstract: Bromodomains (BRDs) are epigenetic interaction domains currently recognized as emerging drug targets for development of anticancer or anti-inflammatory agents. In this study, development of a selective ligand of the fifth BRD of polybromo protein-1 (PB1(5)) related to switch/sucrose nonfermenting (SWI/SNF) chromatin remodeling complexes is presented. A compound collection was evaluated by consensus virtual screening and a hit was identified. The biophysical study of protein–ligand interactions was performed using X-ray crystallography and isothermal titration calorimetry. Collective data supported the hypothesis that affinity improvement could be achieved by enhancing interactions of the complex with the solvent. The derived SAR along with free energy calculations and a consensus hydration analysis using WaterMap and SZmap algorithms guided rational design of a set of novel analogues. The most potent analogue demonstrated high affinity of 3.3 μM and an excellent selectivity profile, thus comprising a promising lead for the development of chemical probes targeting PB1(5).
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Oct 2016
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