I03-Macromolecular Crystallography
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Benjamin J.
Eduful
,
Sean N.
O'Byrne
,
Louisa
Temme
,
Christopher R. M.
Asquith
,
Yi
Liang
,
Alfredo
Picado
,
Joseph R.
Pilotte
,
Mohammad Anwar
Hossain
,
Carrow I.
Wells
,
William J.
Zuercher
,
Carolina M. C.
Catta-Preta
,
Priscila
Zonzini Ramos
,
André De S.
Santiago
,
Rafael M.
Counago
,
Christopher G.
Langendorf
,
Kévin
Nay
,
Jonathan S.
Oakhill
,
Thomas L.
Pulliam
,
Chenchu
Lin
,
Dominik
Awad
,
Timothy M.
Willson
,
Daniel E.
Frigo
,
John W.
Scott
,
David H.
Drewry
Diamond Proposal Number(s):
[10619]
Open Access
Abstract: CAMKK2 is a serine/threonine kinase and an activator of AMPK whose dysregulation is linked with multiple diseases. Unfortunately, STO-609, the tool inhibitor commonly used to probe CAMKK2 signaling, has limitations. To identify promising scaffolds as starting points for the development of high-quality CAMKK2 chemical probes, we utilized a hinge-binding scaffold hopping strategy to design new CAMKK2 inhibitors. Starting from the potent but promiscuous disubstituted 7-azaindole GSK650934, a total of 32 compounds, composed of single-ring, 5,6-, and 6,6-fused heteroaromatic cores, were synthesized. The compound set was specifically designed to probe interactions with the kinase hinge-binding residues. Compared to GSK650394 and STO-609, 13 compounds displayed similar or better CAMKK2 inhibitory potency in vitro, while compounds 13g and 45 had improved selectivity for CAMKK2 across the kinome. Our systematic survey of hinge-binding chemotypes identified several potent and selective inhibitors of CAMKK2 to serve as starting points for medicinal chemistry programs.
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Jul 2021
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I03-Macromolecular Crystallography
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Yuguang
Zhao
,
Fredrik
Svensson
,
David
Steadman
,
Sarah
Frew
,
Amy
Monaghan
,
Magda
Bictash
,
Tiago
Moreira
,
Rod
Chalk
,
Weixian
Lu
,
Paul V.
Fish
,
E. Yvonne
Jones
Diamond Proposal Number(s):
[19946]
Open Access
Abstract: The carboxylesterase Notum hydrolyzes a palmitoleate moiety from Wingless/Integrated(Wnt) ligands and deactivates Wnt signaling. Notum inhibitors can restore Wnt signaling which may be of therapeutic benefit for pathologies such as osteoporosis and Alzheimer’s disease. We report the identification of a novel class of covalent Notum inhibitors, 4-(indolin-1-yl)-4-oxobutanoate esters. High-resolution crystal structures of the Notum inhibitor complexes reveal a common covalent adduct formed between the nucleophile serine-232 and hydrolyzed butyric esters. The covalent interaction in solution was confirmed by mass spectrometry analysis. Inhibitory potencies vary depending on the warheads used. Mechanistically, the resulting acyl-enzyme intermediate carbonyl atom is positioned at an unfavorable angle for the approach of the active site water, which, combined with strong hydrophobic interactions with the enzyme pocket residues, hinders the intermediate from being further processed and results in covalent inhibition. These insights into Notum catalytic inhibition may guide development of more potent Notum inhibitors.
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Jul 2021
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Hector
Newman
,
Alen
Krajnc
,
Domenico
Bellini
,
Charles J.
Eyermann
,
Grant A.
Boyle
,
Neil
Paterson
,
Katherine E.
Mcauley
,
Robert
Lesniak
,
Mukesh
Gangar
,
Frank
Von Delft
,
Jurgen
Brem
,
Kelly
Chibale
,
Christopher J.
Schofield
,
Christopher G.
Dowson
Diamond Proposal Number(s):
[17884]
Open Access
Abstract: The effectiveness of β-lactam antibiotics is increasingly compromised by β-lactamases. Boron-containing inhibitors are potent serine-β-lactamase inhibitors, but the interactions of boron-based compounds with the penicillin-binding protein (PBP) β-lactam targets have not been extensively studied. We used high-throughput X-ray crystallography to explore reactions of a boron-containing fragment set with the Pseudomonas aeruginosa PBP3 (PaPBP3). Multiple crystal structures reveal that boronic acids react with PBPs to give tricovalently linked complexes bonded to Ser294, Ser349, and Lys484 of PaPBP3; benzoxaboroles react with PaPBP3 via reaction with two nucleophilic serines (Ser294 and Ser349) to give dicovalently linked complexes; and vaborbactam reacts to give a monocovalently linked complex. Modifications of the benzoxaborole scaffold resulted in a moderately potent inhibition of PaPBP3, though no antibacterial activity was observed. Overall, the results further evidence the potential for the development of new classes of boron-based antibiotics, which are not compromised by β-lactamase-driven resistance.
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Jul 2021
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
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Francesco
Rianjongdee
,
Stephen J.
Atkinson
,
Chun-Wa
Chung
,
Paola
Grandi
,
James R. J.
Gray
,
Laura J.
Kaushansky
,
Patricia
Medeiros
,
Cassie
Messenger
,
Alex
Phillipou
,
Alex
Preston
,
Rab K.
Prinjha
,
Inmaculada
Rioja
,
Alexander L.
Satz
,
Simon
Taylor
,
Ian D.
Wall
,
Robert J.
Watson
,
Gang
Yao
,
Emmanuel H.
Demont
Abstract: Second-generation bromodomain and extra terminal (BET) inhibitors, which selectively target one of the two bromodomains in the BET proteins, have begun to emerge in the literature. These inhibitors aim to help determine the roles and functions of each domain and assess whether they can demonstrate an improved safety profile in clinical settings compared to pan-BET inhibitors. Herein, we describe the discovery of a novel BET BD2-selective chemotype using a structure-based drug design from a hit identified by DNA-encoded library technologies, showing a structural differentiation from key previously reported greater than 100-fold BD2-selective chemotypes GSK620, GSK046, and ABBV-744. Following a structure-based hypothesis for the selectivity and optimization of the physicochemical properties of the series, we identified 60 (GSK040), an in vitro ready and in vivo capable BET BD2-inhibitor of unprecedented selectivity (5000-fold) against BET BD1, excellent selectivity against other bromodomains, and good physicochemical properties. This novel chemical probe can be added to the toolbox used in the advancement of epigenetics research.
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Jul 2021
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
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Lee A.
Harrison
,
Stephen J.
Atkinson
,
Anna
Bassil
,
Chun-Wa
Chung
,
Paola
Grandi
,
James R. J.
Gray
,
Etienne
Levernier
,
Antonia
Lewis
,
David
Lugo
,
Cassie
Messenger
,
Anne-Marie
Michon
,
Darren J.
Mitchell
,
Alex
Preston
,
Rab K.
Prinjha
,
Inmaculada
Rioja
,
Jonathan T.
Seal
,
Simon
Taylor
,
Ian D.
Wall
,
Robert J.
Watson
,
James M.
Woolven
,
Emmanuel H.
Demont
Abstract: Domain-specific BET bromodomain ligands represent an attractive target for drug discovery with the potential to unlock the therapeutic benefits of antagonizing these proteins without eliciting the toxicological aspects seen with pan-BET inhibitors. While we have reported several distinct classes of BD2 selective compounds, namely, GSK620, GSK549, and GSK046, only GSK046 shows high aqueous solubility. Herein, we describe the lead optimization of a further class of highly soluble compounds based upon a picolinamide chemotype. Focusing on achieving >1000-fold selectivity for BD2 over BD1 ,while retaining favorable physical chemical properties, compound 36 was identified as being 2000-fold selective for BD2 over BD1 (Brd4 data) with >1 mg/mL solubility in FaSSIF media. 36 represents a valuable new in vivo ready molecule for the exploration of the BD2 phenotype.
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Jul 2021
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I02-Macromolecular Crystallography
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Simon C. C.
Lucas
,
Stephen J.
Atkinson
,
Chun-Wa
Chung
,
Rob
Davis
,
Laurie
Gordon
,
Paola
Grandi
,
James J. R.
Gray
,
Thomas
Grimes
,
Alexander
Phillipou
,
Alex G.
Preston
,
Rab K.
Prinjha
,
Inmaculada
Rioja
,
Simon
Taylor
,
Nicholas C. O.
Tomkinson
,
Ian
Wall
,
Robert J.
Watson
,
James
Woolven
,
Emmanuel H.
Demont
Abstract: Herein, a series of 2,3-dihydrobenzofurans have been developed as highly potent bromo and extra-terminal domain (BET) inhibitors with 1000-fold selectivity for the second bromodomain (BD2) over the first bromodomain (BD1). Investment in the development of two orthogonal synthetic routes delivered inhibitors that were potent and selective but had raised in vitro clearance and suboptimal solubility. Insertion of a quaternary center into the 2,3-dihydrobenzofuran core blocked a key site of metabolism and improved the solubility. This led to the development of inhibitor 71 (GSK852): a potent, 1000-fold-selective, highly soluble compound with good in vivo rat and dog pharmacokinetics.
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Jul 2021
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I03-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Open Access
Abstract: Protein–protein modulation has emerged as a proven approach to drug discovery. While significant progress has been gained in developing protein–protein interaction (PPI) inhibitors, the orthogonal approach of PPI stabilization lacks established methodologies for drug design. Here, we report the systematic ″bottom-up″ development of a reversible covalent PPI stabilizer. An imine bond was employed to anchor the stabilizer at the interface of the 14-3-3/p65 complex, leading to a molecular glue that elicited an 81-fold increase in complex stabilization. Utilizing protein crystallography and biophysical assays, we deconvoluted how chemical properties of a stabilizer translate to structural changes in the ternary 14-3-3/p65/molecular glue complex. Furthermore, we explore how this leads to high cooperativity and increased stability of the complex.
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Jun 2021
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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David
Lee Walmsley
,
James B.
Murray
,
Pawel
Dokurno
,
Andrew J.
Massey
,
Karen
Benwell
,
Andrea
Fiumana
,
Nicolas
Foloppe
,
Stuart
Ray
,
Julia
Smith
,
Allan E.
Surgenor
,
Thomas
Edmonds
,
Didier
Demarles
,
Mike
Burbridge
,
Francisco
Cruzalegui
,
Andras
Kotschy
,
Roderick E.
Hubbard
Open Access
Abstract: The serine/threonine kinase DYRK1A has been implicated in regulation of a variety of cellular processes associated with cancer progression, including cell cycle control, DNA damage repair, protection from apoptosis, cell differentiation, and metastasis. In addition, elevated-level DYRK1A activity has been associated with increased severity of symptoms in Down’s syndrome. A selective inhibitor of DYRK1A could therefore be of therapeutic benefit. We have used fragment and structure-based discovery methods to identify a highly selective, well-tolerated, brain-penetrant DYRK1A inhibitor which showed in vivo activity in a tumor model. The inhibitor provides a useful tool compound for further exploration of the effect of DYRK1A inhibition in models of disease.
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Jun 2021
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I04-Macromolecular Crystallography
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Mujtaba
Hassan
,
Sjors
Van Klaveren
,
Maria
Håkansson
,
Carl
Diehl
,
Rebeka
Kovačič
,
Floriane
Baussière
,
Anders
Sundin
,
Jaka
Dernovšek
,
Björn
Walse
,
Fredrik
Zetterberg
,
Hakon
Leffler
,
Marko
Anderluh
,
Tihomir
Tomašič
,
Žiga
Jakopin
,
Ulf J.
Nilsson
Diamond Proposal Number(s):
[23282]
Abstract: We have obtained the X-ray crystal structure of the galectin-8 N-terminal domain (galectin-8N) with a previously reported quinoline–galactoside ligand at a resolution of 1.6 Å. Based on this X-ray structure, a collection of galactosides derivatised at O3 with triazole, benzimidazole, benzothiazole, and benzoxazole moieties were designed and synthesised. This led to the discovery of a 3-O-(N-methylbenzimidazolylmethyl)–galactoside with a Kd of 1.8 μM for galectin-8N, the most potent selective synthetic galectin-8N ligand to date. Molecular dynamics simulations showed that benzimidazole–galactoside derivatives bind the non-conserved amino acid Gln47, accounting for the higher selectivity for galectin-8N. Galectin-8 is a carbohydrate-binding protein that plays a key role in pathological lymphangiogenesis, modulation of the immune system, and autophagy. Thus, the benzimidazole-derivatised galactosides represent promising compounds for studies of the pathological implications of galectin-8, as well as a starting point for the development of anti-tumour and anti-inflammatory therapeutics targeting galectin-8.
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Jun 2021
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Douglas S.
Williamson
,
Garrick P.
Smith
,
Gitte K.
Mikkelsen
,
Thomas
Jensen
,
Pamela
Acheson-Dossang
,
Lassina
Badolo
,
Simon T.
Bedford
,
Victoria
Chell
,
I-Jen
Chen
,
Pawel
Dokurno
,
Morten
Hentzer
,
Stephanie
Newland
,
Stuart C.
Ray
,
Terry
Shaw
,
Allan E.
Surgenor
,
Lindsey
Terry
,
Yikang
Wang
,
Kenneth V.
Christensen
Diamond Proposal Number(s):
[27063, 2103, 5791, 6001]
Open Access
Abstract: Inhibitors of leucine-rich repeat kinase 2 (LRRK2) and mutants, such as G2019S, have potential utility in Parkinson’s disease treatment. Fragment hit-derived pyrrolo[2,3-d]pyrimidines underwent optimization using X-ray structures of LRRK2 kinase domain surrogates, based on checkpoint kinase 1 (CHK1) and a CHK1 10-point mutant. (2R)-2-Methylpyrrolidin-1-yl derivative 18 (LRRK2 G2019S cKi 0.7 nM, LE 0.66) was identified, with increased potency consistent with an X-ray structure of 18/CHK1 10-pt. mutant showing the 2-methyl substituent proximal to Ala147 (Ala2016 in LRRK2). Further structure-guided elaboration of 18 gave the 2-[(1,3-dimethyl-1H-pyrazol-4-yl)amino] derivative 32. Optimization of 32 afforded diastereomeric oxolan-3-yl derivatives 44 and 45, which demonstrated a favorable in vitro PK profile, although they displayed species disconnects in the in vivo PK profile, and a propensity for P-gp- and/or BCRP-mediated efflux in a mouse model. Compounds 44 and 45 demonstrated high potency and exquisite selectivity for LRRK2 and utility as chemical probes for the study of LRRK2 inhibition.
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Jun 2021
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