I24-Microfocus Macromolecular Crystallography
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Stacey M.
Southall
,
Joydeep
Banerjee
,
Jason
Brown
,
Kristina
Butkovic
,
Andrew D.
Cansfield
,
Julie E.
Cansfield
,
Miles S.
Congreve
,
Gabriella
Cseke
,
Francesca
Deflorian
,
Martina Petrovic
Hunjadi
,
Antun
Hutinec
,
Trinadh Kumar
Inturi
,
Renata
Rupcic
,
Gordon
Saxty
,
Stephen P.
Watson
Abstract: The diastereomeric macrocyclic calcitonin gene-related peptide (CGRP) antagonists HTL0029881 (3) and HTL0029882 (4), in which the stereochemistry of a spiro center is reversed, surprisingly demonstrate comparable potency. X-ray crystallographic characterization demonstrates that 3 binds to the CGRP receptor in a precedented manner but that 4 binds in an unprecedented, unexpected, and radically different manner. The observation of this phenomenon is noteworthy and may open novel avenues for CGRP receptor antagonist design.
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Nov 2022
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I24-Microfocus Macromolecular Crystallography
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Indran
Mathavan
,
Lawrence J.
Liu
,
Sean W.
Robinson
,
Nelly
El-Sakkary
,
Adam Jo J.
Elatico
,
Darwin
Gomez
,
Ricky
Nellas
,
Raymond J.
Owens
,
William
Zuercher
,
Iva
Navratilova
,
Conor R.
Caffrey
,
Konstantinos
Beis
Diamond Proposal Number(s):
[12579]
Open Access
Abstract: Schistosomiasis is a neglected tropical disease caused by parasitic flatworms. Current treatment relies on just one partially effective drug, praziquantel (PZQ). Schistosoma mansoni Venus Kinase Receptors 1 and 2 (SmVKR1 and SmVKR2) are important for parasite growth and egg production, and are potential targets for combating schistosomiasis. VKRs consist of an extracellular Venus Flytrap Module (VFTM) linked via a transmembrane helix to a kinase domain. Here, we initiated a drug discovery effort to inhibit the activity of the SmVKR2 kinase domain (SmVKR2KD) by screening the GSK published kinase inhibitor set 2 (PKIS2). We identified several inhibitors, of which four were able to inhibit its enzymatic activity and induced phenotypic changes in ex vivoS. mansoni. Our crystal structure of the SmVKR2KD displays an active-like state that sheds light on the activation process of VKRs. Our data provide a basis for the further exploration of SmVKR2 as a possible drug target.
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Oct 2022
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Emiliano
Tamanini
,
Shin
Miyamura
,
Ildiko M.
Buck
,
Benjamin D.
Cons
,
Lee
Dawson
,
Charlotte
East
,
Takashi
Futamura
,
Shintaro
Goto
,
Charlotte
Griffiths-Jones
,
Tetsuya
Hashimoto
,
Tom D.
Heightman
,
Shunpei
Ishikawa
,
Hideki
Ito
,
Yosuke
Kaneko
,
Tatsuya
Kawato
,
Kazumi
Kondo
,
Naoki
Kurihara
,
James M.
Mccarthy
,
Yukiko
Mori
,
Tsuyoshi
Nagase
,
Yuichiro
Nakaishi
,
Judith
Reeks
,
Akimasa
Sato
,
Patrick
Schöpf
,
Kuninori
Tai
,
Taichi
Tamai
,
Dominic
Tisi
,
Alison J.-A.
Woolford
Abstract: Fragment-based ligand discovery was successfully applied to histone deacetylase HDAC2. In addition to the anticipated hydroxamic acid- and benzamide-based fragment screening hits, a low affinity (∼1 mM) α-amino-amide zinc binding fragment was identified, as well as fragments binding to other regions of the catalytic site. This alternative zinc-binding fragment was further optimized, guided by the structural information from protein–ligand complex X-ray structures, into a sub-μM, brain penetrant, HDAC2 inhibitor (17) capable of modulating histone acetylation levels in vivo.
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Sep 2022
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I03-Macromolecular Crystallography
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Frederick W.
Goldberg
,
Attilla K. T.
Ting
,
David
Beattie
,
Gillian M.
Lamont
,
Charlene
Fallan
,
M. Raymond V.
Finlay
,
Beth
Williamson
,
Marianne
Schimpl
,
Alexander R.
Harmer
,
Oladipupo B.
Adeyemi
,
Pär
Nordell
,
Anna S.
Cronin
,
Mercedes
Vazquez-Chantada
,
Derek
Barratt
,
Antonio
Ramos-Montoya
,
Elaine B.
Cadogan
,
Barry R.
Davies
Diamond Proposal Number(s):
[20015]
Abstract: The DNA-PK complex is activated by double-strand DNA breaks and regulates the non-homologous end-joining repair pathway; thus, targeting DNA-PK by inhibiting the DNA-PK catalytic subunit (DNA-PKcs) is potentially a useful therapeutic approach for oncology. A previously reported series of neutral DNA-PKcs inhibitors were modified to incorporate a basic group, with the rationale that increasing the volume of distribution while maintaining good metabolic stability should increase the half-life. However, adding a basic group introduced hERG activity, and basic compounds with modest hERG activity (IC50 = 10–15 μM) prolonged QTc (time from the start of the Q wave to the end of the T wave, corrected by heart rate) in an anaesthetized guinea pig cardiovascular model. Further optimization was necessary, including modulation of pKa, to identify compound 18, which combines low hERG activity (IC50 = 75 μM) with excellent kinome selectivity and favorable pharmacokinetic properties.
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Jul 2022
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I03-Macromolecular Crystallography
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Mujtaba
Hassan
,
Floriane
Baussière
,
Samo
Guzelj
,
Anders P.
Sundin
,
Maria
Håkansson
,
Rebeka
Kovačič
,
Hakon
Leffler
,
Tihomir
Tomašič
,
Marko
Anderluh
,
Žiga
Jakopin
,
Ulf J.
Nilsson
Diamond Proposal Number(s):
[15916]
Open Access
Abstract: Galectin-8 is a carbohydrate-binding protein that plays a crucial role in tumor progression and metastasis, antibacterial autophagy, modulation of the immune system, and bone remodeling. The design, synthesis, and protein affinity evaluation of a set of C-3 substituted benzimidazole and quinoline d-galactal derivatives identified a d-galactal-benzimidazole hybrid as a selective ligand for the galectin-8 N-terminal domain (galectin-8N), with a Kd of 48 μM and 15-fold selectivity over galectin-3 and even better selectivity over the other mammalian galectins. X-ray structural analysis of galectin-8N in complex with one benzimidazole- and one quinoline-galactal derivative at 1.52 and 2.1 Å together with molecular dynamics simulations and quantum mechanical calculations of galectin-8N in complex with the benzimidazole derivative revealed orbital overlap between a NH LUMO of Arg45 with electron rich HOMOs of the olefin and O4 of the d-galactal. Such overlap is hypothesized to contribute to the high affinity of the d-galactal-derived ligands for galectin-8N. A (3-(4,5-dimethylthiazol-2-yl)-5-(3- carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) (MTS) assay evaluation of the d-galactal-benzimidazole hybrid and an analogous galactoside derivative on a panel of cell lines with MTS assay showed no effect on cell viability up to 100 μM concentration. A subsequent functional assay using the MDA-MB-231 cell line demonstrated that the d-galactal-benzimidazole hybrid and the analogous galactoside derivative reduced the secretion of the proinflammatory cytokines interleukin-6 (IL-6) and IL-8 in a dose-dependent manner. Therefore, these compounds represent potential probes for galectin-8N pharmacology investigations and possibly promising leads for the design and synthesis of potent and selective galectin-8 inhibitors as potential antitumor and anti-inflammatory agents.
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Nov 2021
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Derun
Li
,
Yongqi
Deng
,
Abdelghani
Achab
,
Indu
Bharathan
,
Brett Andrew
Hopkins
,
Wensheng
Yu
,
Hongjun
Zhang
,
Sulagna
Sanyal
,
Qinglin
Pu
,
Hua
Zhou
,
Kun
Liu
,
Jongwon
Lim
,
Xavier
Fradera
,
Charles A.
Lesburg
,
Alfred
Lammens
,
Theodore A.
Martinot
,
Ryan D.
Cohen
,
Amy C.
Doty
,
Heidi
Ferguson
,
Elliott B.
Nickbarg
,
Mangeng
Cheng
,
Peter
Spacciapoli
,
Prasanthi
Geda
,
Xuelei
Song
,
Nadya
Smotrov
,
Pravien
Abeywickrema
,
Christine
Andrews
,
Chad
Chamberlin
,
Omar
Mabrouk
,
Patrick
Curran
,
Matthew
Richards
,
Peter
Saradjian
,
J. Richard
Miller
,
Ian
Knemeyer
,
Karin M.
Otte
,
Stella
Vincent
,
Nunzio
Sciammetta
,
Alexander
Pasternak
,
David Jonathan
Bennett
,
Yongxin
Han
Abstract: Indoleamine-2,3-dioxygenase-1 (IDO1) has emerged as an attractive target for cancer immunotherapy. An automated ligand identification system screen afforded the tetrahydroquinoline class of novel IDO1 inhibitors. Potency and pharmacokinetic (PK) were key issues with this class of compounds. Structure-based drug design and strategic incorporation of polarity enabled the rapid improvement on potency, solubility, and oxidative metabolic stability. Metabolite identification studies revealed that amide hydrolysis in the D-pocket was the key clearance mechanism for this class. Strategic survey of amide isosteres revealed that carbamates and N-pyrimidines, which maintained exquisite potencies, mitigated the amide hydrolysis issue and led to an improved rat PK profile. The lead compound 28 is a potent IDO1 inhibitor, with clean off-target profiles and the potential for quaque die dosing in humans.
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Mar 2021
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I03-Macromolecular Crystallography
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Brandon A.
Vara
,
Samuel M.
Levi
,
Abdelghani
Achab
,
David A.
Candito
,
Xavier
Fradera
,
Charles A.
Lesburg
,
Shuhei
Kawamura
,
Brian M.
Lacey
,
Jongwon
Lim
,
Joey L.
Methot
,
Zangwei
Xu
,
Haiyan
Xu
,
Dustin M.
Smith
,
Jennifer A.
Piesvaux
,
J. Richard
Miller
,
Mark
Bittinger
,
Sheila H.
Ranganath
,
David J.
Bennett
,
Erin F.
Dimauro
,
Alexander
Pasternak
Abstract: Hematopoietic progenitor kinase 1 (HPK1), a serine/threonine kinase, is a negative immune regulator of T cell receptor (TCR) and B cell signaling that is primarily expressed in hematopoietic cells. Accordingly, it has been reported that HPK1 loss-of-function in HPK1 kinase-dead syngeneic mouse models shows enhanced T cell signaling and cytokine production as well as tumor growth inhibition in vivo, supporting its value as an immunotherapeutic target. Herein, we present the structurally enabled discovery of novel, potent, and selective diaminopyrimidine carboxamide HPK1 inhibitors. The key discovery of a carboxamide moiety was essential for enhanced enzyme inhibitory potency and kinome selectivity as well as sustained elevation of cellular IL-2 production across a titration range in human peripheral blood mononuclear cells. The elucidation of structure–activity relationships using various pendant amino ring systems allowed for the identification of several small molecule type-I inhibitors with promising in vitro profiles.
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Mar 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Gavin W.
Collie
,
Iacovos N.
Michaelides
,
Kevin
Embrey
,
Christopher J.
Stubbs
,
Ulf
Börjesson
,
Ian L.
Dale
,
Arjan
Snijder
,
Louise
Barlind
,
Kun
Song
,
Puneet
Khurana
,
Christopher
Phillips
,
R. Ian
Storer
Open Access
Abstract: We report here a fragment screen directed toward the c-MET kinase from which we discovered a series of inhibitors able to bind to a rare conformation of the protein in which the P-loop adopts a collapsed, or folded, arrangement. Preliminary SAR exploration led to an inhibitor (7) with nanomolar biochemical activity against c-MET and promising cell activity and kinase selectivity. These findings increase our structural understanding of the folded P-loop conformation of c-MET and provide a sound structural and chemical basis for further investigation of this underexplored yet potentially therapeutically exploitable conformational state.
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Dec 2020
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[11235]
Abstract: Competitive inhibitors of galactocerebrosidase (GALC) could be candidates for pharmacological chaperone therapy of patients with Krabbe disease. The known and selective nortropane-type iminosugar galacto-noeurostegine has been found to competitively inhibit GALC with Ki = 7 μM at pH 4.6, which is 330-fold more potent than the analogous deoxynoeurostegine. It was shown through X-ray protein crystallography that galacto-noeurostegine binds to the active site of GALC in its bicyclic form.
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Dec 2020
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I04-Macromolecular Crystallography
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Žiga
Skok
,
Michaela
Barančoková
,
Ondřej
Benek
,
Cristina
Durante Cruz
,
Päivi
Tammela
,
Tihomir
Tomašič
,
Nace
Zidar
,
Lucija Peterlin
Mašič
,
Anamarija
Zega
,
Clare E. M.
Stevenson
,
Julia E. A.
Mundy
,
David M.
Lawson
,
Anthony
Maxwell
,
Danijel
Kikelj
,
Janez
Ilaš
Diamond Proposal Number(s):
[18565]
Open Access
Abstract: We designed and synthesized a series of inhibitors of the bacterial enzymes DNA gyrase and DNA topoisomerase IV, based on our recently published benzothiazole-based inhibitor bearing an oxalyl moiety. To improve the antibacterial activity and retain potent enzymatic activity, we systematically explored the chemical space. Several strategies of modification were followed: varying substituents on the pyrrole carboxamide moiety, alteration of the central scaffold, including variation of substitution position and, most importantly, modification of the oxalyl moiety. Compounds with acidic, basic, and neutral properties were synthesized. To understand the mechanism of action and binding mode, we have obtained a crystal structure of compound 16a, bearing a primary amino group, in complex with the N-terminal domain of E. coli gyrase B (24 kDa) (PDB: 6YD9). Compound 15a, with a low molecular weight of 383 Da, potent inhibitory activity on E. coli gyrase (IC50 = 9.5 nM), potent antibacterial activity on E. faecalis (MIC = 3.13 μM), and efflux impaired E. coli strain (MIC = 0.78 μM), is an important contribution for the development of novel gyrase and topoisomerase IV inhibitors in Gram-negative bacteria.
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Oct 2020
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