I02-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[442]
Abstract: Selectivity remains a challenge for ATP-mimetic kinase inhibitors, an issue that may be overcome by targeting unique residues or binding pockets. However, to date only few strategies have been developed. Here we identify that bulky residues located N-terminal to the DFG motif (DFG-1) represent an opportunity for designing highly selective inhibitors with unexpected binding modes. We demonstrate that several diverse inhibitors exerted selective, non-canonical binding modes that exclusively target large hydrophobic DFG-1 residues present in many kinases including PIM, CK1, DAPK and CLK. Using the CLK family as a model, structural and biochemical data revealed that the DFG-1 valine controlled a non-canonical binding mode in CLK1, providing a rational for selectivity over the closely-related CLK3 which harbors a smaller DFG-1 alanine. Our data suggests that targeting the restricted back pocket in the small fraction of kinases that harbor bulky DFG-1 residues offers a versatile selectivity filter for inhibitor design.
|
Aug 2020
|
|
I04-1-Macromolecular Crystallography (fixed wavelength)
|
Diamond Proposal Number(s):
[8421]
Open Access
Abstract: Since hyperactivity of the protein kinase DYRK1A is linked to several neurodegenerative disorders, DYRK1A inhibitors have been suggested as potential therapeutics for Down syndrome and Alzheimer’s disease. Most published inhibitors to date suffer from low selectivity against related kinases or from unfavorable physicochemical properties. In order to identify DYRK1A inhibitors with improved properties, a series of new chemicals based on [b]-annulated halogenated indoles were designed, synthesized, and evaluated for biological activity. Analysis of crystal structures revealed a typical type-I binding mode of the new inhibitor 4-chlorocyclohepta[b]indol-10(5H)-one in DYRK1A, exploiting mainly shape complementarity for tight binding. Conversion of the DYRK1A inhibitor 8-chloro-1,2,3,9-tetrahydro-4H-carbazol-4-one into a corresponding Mannich base hydrochloride improved the aqueous solubility but abrogated kinase inhibitory activity.
|
Nov 2019
|
|
I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
|
Eidarus
Salah
,
Deep
Chatterjee
,
Alessandra
Beltrami
,
Anthony
Tumber
,
Franziska
Preuss
,
Peter
Canning
,
Apirat
Chaikuad
,
Petra
Knaus
,
Stefan
Knapp
,
Alex N.
Bullock
,
Sebastian
Mathea
Diamond Proposal Number(s):
[6391, 10619]
Abstract: LIM domain kinase 1 (LIMK1) is a key regulator of actin dynamics. It is thereby a potential therapeutic target for the prevention of fragile X syndrome and amyotrophic lateral sclerosis. Herein, we use X-ray crystallography and activity assays to describe how LIMK1 accomplishes substrate specificity, to suggest a unique 'rock-and-poke' mechanism of catalysis and to explore the regulation of the kinase by activation loop phosphorylation. Based on these findings, a differential scanning fluorimetry assay and a RapidFire mass spectrometry activity assay were established, leading to the discovery and confirmation of a set of small-molecule LIMK1 inhibitors. Interestingly, several of the inhibitors were inactive towards the closely related isoform LIMK2. Finally, crystal structures of the LIMK1 kinase domain in complex with inhibitors (PF-477736 and staurosporine, respectively) are presented, providing insights into LIMK1 plasticity upon inhibitor binding.
|
Oct 2019
|
|
I04-1-Macromolecular Crystallography (fixed wavelength)
|
Sandra
Röhm
,
Benedict-tilman
Berger
,
Martin
Schroeder
,
Apirat
Chaikuad
,
Rob
Winkel
,
Koen F. W.
Hekking
,
Jorg J. C.
Benningshof
,
Gerhard
Müller
,
Roberta
Tesch
,
Mark
Kudolo
,
Michael
Forster
,
Stefan
Laufer
,
Stefan
Knapp
Diamond Proposal Number(s):
[10619]
Abstract: p38 mitogen-activated protein kinases are key mediators of environmental stress response and are promising targets for treatment of inflammatory diseases and cancer. Numerous efforts have led to the discovery of several potent inhibitors; however, so far no highly selective type-II inhibitors have been reported. We previously identified VPC-00628 as a potent and selective type-II inhibitor of p38α/β with few off-targets. Here we analyzed the chemical building blocks of VPC-00628 that played a key role in achieving potency and selectivity through targeting an inactive state of the kinases induced by a unique folded P-loop conformation. Using a rapid, systematic combinatorial synthetic approach, we identified compound 93 (SR-318) with excellent potency and selectivity for p38α/β, which potently inhibited the TNF-α release in whole blood. SR-318 therefore presents a potent and selective type-II inhibitor of p38α/β that can be used as a chemical probe for targeting this particular inactive state of these two p38 isoforms.
|
Oct 2019
|
|
I02-Macromolecular Crystallography
|
Jan S.
Kramer
,
Stefano
Woltersdorf
,
Thomas
Duflot
,
Kerstin
Hiesinger
,
Felix F.
Lillich
,
Felix
Knöll
,
Sandra K.
Wittmann
,
Franca M.
Klingler
,
Steffen
Brunst
,
Apirat
Chaikuad
,
Christophe
Morisseau
,
Bruce D.
Hammock
,
Carola
Buccellati
,
Angelo
Sala
,
G. Enrico
Rovati
,
Matthieu
Leuillier
,
Sylvain
Fraineau
,
Julie
Rondeaux
,
Victor
Hernandez Olmos
,
Jan
Heering
,
Daniel
Merk
,
Denys
Pogoryelov
,
Dieter
Steinhilber
,
Stefan
Knapp
,
Jeremy
Bellien
,
Ewgenij
Proschak
Abstract: The emerging pharmacological target soluble epoxide hydrolase (sEH) is a bifunctional enzyme exhibiting two different catalytic activities, which are located in two distinct domains. Although the physiological role of the C-terminal hydrolase domain is well-investigated, little is known about its phosphatase activity located in the N-terminal domain of the sEH (sEH-P). Herein, we report the discovery and optimization of the first inhibitor of human and rat sEH-P, applicable in vivo. X-ray structure analysis of the sEH phosphatase domain complexed with an inhibitor provides insights in the molecular basis of small-molecule sEH-P inhibition and helps to rationalize the structure-activity relationships. 4-(4-(3,4-Dichlorophenyl)-5-phenyloxazol-2-yl)butanoic acid (22b, SWE101) has an excellent pharmacokinetic and pharmacodynamic profile in rats and enables the investigation of the physiological and pathophysiological role of sEH-P in vivo.
|
Aug 2019
|
|
I02-Macromolecular Crystallography
|
Sven
Verdonck
,
Szu-yuan
Pu
,
Fiona J.
Sorrell
,
Jon M.
Elkins
,
Mathy
Froeyen
,
Ling-jie
Gao
,
Laura I.
Prugar
,
Danielle E.
Dorosky
,
Jennifer M.
Brannan
,
Rina
Barouch-bentov
,
Stefan
Knapp
,
John M.
Dye
,
Piet
Herdewijn
,
Shirit
Einav
,
Steven
De Jonghe
Diamond Proposal Number(s):
[10619]
Abstract: There are currently no approved drugs for the treatment of emerging viral infections, such as dengue and Ebola. Adaptor-associated kinase 1 (AAK1) is a cellular serine–threonine protein kinase that functions as a key regulator of the clathrin-associated host adaptor proteins and regulates the intracellular trafficking of multiple unrelated RNA viruses. Moreover, AAK1 is overexpressed specifically in dengue virus-infected but not bystander cells. Because AAK1 is a promising antiviral drug target, we have embarked on an optimization campaign of a previously identified 7-azaindole analogue, yielding novel pyrrolo[2,3-b]pyridines with high AAK1 affinity. The optimized compounds demonstrate improved activity against dengue virus both in vitro and in human primary dendritic cells and the unrelated Ebola virus. These findings demonstrate that targeting cellular AAK1 may represent a promising broad-spectrum antiviral strategy.
|
May 2019
|
|
I03-Macromolecular Crystallography
|
Melissa
D'ascenzio
,
Kathryn M.
Pugh
,
Rebecca
Konietzny
,
Georgina
Berridge
,
Cynthia
Tallant
,
Shaima
Hashem
,
Octovia
Monteiro
,
Jason R.
Thomas
,
Markus
Schirle
,
Stefan
Knapp
,
Brian
Marsden
,
Oleg
Fedorov
,
Chas
Bountra
,
Benedikt M.
Kessler
,
Paul E.
Brennan
Diamond Proposal Number(s):
[10619]
Open Access
Abstract: Bromodomain‐containing proteins are epigenetic modulators involved in a wide range of cellular processes, from recruitment of transcription factors to pathological disruption of gene regulation and cancer development. Since the druggability of these acetyl‐lysine reader domains was established, efforts were made to develop potent and selective inhibitors across the entire family. Here we report the development of a small molecule‐based approach to covalently modify recombinant and endogenous bromodomain‐containing proteins by targeting a conserved lysine and a tyrosine residue in the variable ZA or BC loops. Moreover, the addition of a reporter tag allowed in‐gel visualization and pull‐down of the desired bromodomains.
|
Jan 2019
|
|
I02-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
|
Václav
Němec
,
Michaela
Hylsová
,
Lukáš
Maier
,
Jana
Flegel
,
Sonja
Sievers
,
Slava
Ziegler
,
Martin
Schroeder
,
Benedict-tilman
Berger
,
Apirat
Chaikuad
,
Barbora
Valčíková
,
Stjepan
Uldrijan
,
Stanislav
Drápela
,
Karel
Souček
,
Herbert
Waldmann
,
Stefan
Knapp
,
Kamil
Paruch
Diamond Proposal Number(s):
[10619]
Abstract: Reported is the identification of the furo[3,2‐b]pyridine core as a novel scaffold for potent and highly selective inhibitors of cdc‐like kinases (CLKs) and efficient modulators of the Hedgehog signaling pathway. Initially, a diverse target compound set was prepared by synthetic sequences based on chemoselective metal‐mediated couplings, including assembly of the furo[3,2‐b]pyridine scaffold by copper‐mediated oxidative cyclization. Optimization of the subseries containing 3,5‐disubstituted furo[3,2‐b]pyridines afforded potent, cell‐active, and highly selective inhibitors of CLKs. Profiling of the kinase‐inactive subset of 3,5,7‐trisubstituted furo[3,2‐b]pyridines revealed sub‐micromolar modulators of the Hedgehog pathway.
|
Dec 2018
|
|
I04-Macromolecular Crystallography
|
Diamond Proposal Number(s):
[105433]
Abstract: Lysine acetylation is an epigenetic mark that is principally recognized by bromodomains and recently structurally diverse YEATS domains also emerged as readers of lysine acetyl/acylations. Here we present a crystallography-based strategy and the discovery of fragments binding to the ENL YEATS domain, a potential drug target. Crystal structures combined with synthetic efforts led to the identification of a sub-micromolar binder, providing first starting points for the development of chemical probes for this reader domain family.
|
Nov 2018
|
|
|
|
Moses
Moustakim
,
Thomas
Christott
,
Octovia P.
Monteiro
,
James
Bennett
,
Charline
Giroud
,
Jennifer
Ward
,
Catherine M.
Rogers
,
Paul
Smith
,
Ioanna
Panagakou
,
Laura
Diaz-saez
,
Suet Ling
Felce
,
Vicki
Gamble
,
Carina
Gileadi
,
Nadia
Halidi
,
David
Heidenreich
,
Apirat
Chaikuad
,
Stefan
Knapp
,
Kilian V. M.
Huber
,
Gillian
Farnie
,
Jag
Heer
,
Nenad
Manevski
,
Gennady
Poda
,
Rima
Al-awar
,
Darren J.
Dixon
,
Paul E.
Brennan
,
Oleg
Fedorov
Abstract: YEATS domain (YD) containing proteins are an emerging class of epigenetic targets in drug discovery. Dysregulation of these modified lysine‐binding proteins has been linked to the onset and progression of cancers. We herein report the discovery and characterisation of the first small‐molecule chemical probe, SGC‐iMLLT, for the YD of MLLT1 (ENL/YEATS1) and MLLT3 (AF9/YEATS3). SGC‐iMLLT is a potent and selective inhibitor of MLLT1/3–histone interactions. Excellent selectivity over other human YD proteins (YEATS2/4) and bromodomains was observed. Furthermore, our probe displays cellular target engagement of MLLT1 and MLLT3. The first small‐molecule X‐ray co‐crystal structures with the MLLT1 YD are also reported. This first‐in‐class probe molecule can be used to understand MLLT1/3‐associated biology and the therapeutic potential of small‐molecule YD inhibitors.
|
Oct 2018
|
|
