I03-Macromolecular Crystallography
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Joanna L.
Chen
,
Joey L.
Methot
,
Matthew J.
Mitcheltree
,
Andrew
Musacchio
,
Emily B.
Corcoran
,
Guo
Feng
,
Alfred
Lammens
,
Klaus
Maskos
,
Rachel L.
Palte
,
Meredith M.
Rickard
,
Karin M.
Otte
,
My S.
Mansueto
,
Sriraman
Venkat
,
Christopher
Sondey
,
Maren
Thomsen
,
Charles A.
Lesburg
,
Xavier
Fradera
,
Matthew J.
Fell
,
Erin F.
Dimauro
,
Phieng
Siliphaivanh
Abstract: Receptor-interacting protein kinase 1 (RIPK1) plays an essential role in necroptosis, a form of inflammatory, caspase-independent, programmed cell death. Allosteric inhibitors of RIPK1 have been shown to block necroptotic cell death and thus may offer potential therapeutic opportunities across a range of infectious, autoimmune, and neurodegenerative diseases. We report the structure-informed discovery of a novel series of bridged benzoazepine amides as part of our efforts to develop a CNS-penetrant small-molecule inhibitor of RIPK1 with a low projected oral human dose.
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May 2025
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I03-Macromolecular Crystallography
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Jeffrey A.
Boerth
,
Marianne
Schimpl
,
Simon C. C.
Lucas
,
Jingwen
Zhang
,
Erin L.
Code
,
Kevin J.
Embrey
,
Philip B.
Rawlins
,
Haixia
Wang
,
R. Ian
Storer
,
Paolo
Di Fruscia
,
Jennifer E.
Nelson
,
Alexander G.
Milbradt
,
Ulf
Börjesson
,
Andrea
Gohlke
,
Victoria
Korboukh
,
Ariamala
Gopalsamy
Diamond Proposal Number(s):
[20015]
Abstract: Suppression of oncogenic gene expression is an effective strategy for the treatment of cancer. The SWI/SNF (SWItch/Sucrose Non-Fermentable) complex plays an important role in regulating gene activation or repression, and its dysregulation has been linked to aberrant transcription activity in many types of cancer. Targeting the subunits of this complex, such as SMARCA2, SMARCA4, and PBRM1, which are part of the bromodomain family VIII, has significant therapeutic potential. Herein we report the discovery of pyrimidoindolones as a novel series of bromodomain family VIII binders identified through an NMR-based fragment screen. These binders have been optimized to achieve sub-μM affinity for the family VIII proteins SMARCA2, SMARCA4, and PRBM1, with promising physicochemical properties.
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May 2025
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I04-Macromolecular Crystallography
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Marco
Paolino
,
Giusy
Tassone
,
Paolo
Governa
,
Mario
Saletti
,
Matteo
Lami
,
Riccardo
Carletti
,
Filippo
Sacchetta
,
Cecilia
Pozzi
,
Maurizio
Orlandini
,
Fabrizio
Manetti
,
Massimo
Olivucci
,
Andrea
Cappelli
Diamond Proposal Number(s):
[21741, 29907]
Abstract: The use of Targeted Covalent Inhibitors (TCIs) is an expanding strategy for the development of innovative drugs. It is driven by two fundamental steps: (1) recognition of the target site by the molecule and (2) establishment of the covalent interaction by its reactive group. The development of new TCIs depends on the development of new warheads. Here, we propose the use of Morita–Baylis–Hillman adducts (MBHAs) to covalently bind Lys strategically placed inside a lipophilic pocket. A human cellular retinoic acid binding protein II mutant (M2) was selected as a test bench for a library of 19 MBHAs. The noncovalent interaction step was investigated by molecular docking studies, while experimentally the entire library was incubated with M2 and crystallized to confirm covalent binding with the target lysine. The results, rationalized through covalent docking analysis, support our hypothesis of MBHAs as reactive scaffolds for the design of lysine-TCIs.
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Mar 2025
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I04-Macromolecular Crystallography
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Simon C. C.
Lucas
,
Yong
Xu
,
Sarah
Hewitt
,
Gavin W.
Collie
,
Lucia
Fusani
,
Ganesh
Kadamur
,
Thomas E.
Hadfield
,
Nancy
Su
,
Caroline
Truman
,
Sylvain
Demanze
,
Haie
Hao
,
Christopher
Phillips
Abstract: Most ligands for the Von Hippel–Lindau tumor suppressor (VHL) bind at the HIF-1α binding site. Ligands that bind to allosteric sites on VHL could be highly valuable for the field of protein degradation, therefore, a covalent hit identification campaign was run targeting Cys77 on VHL. Hit 2 bound selectively to Cys77 on VHL and did not alkylate the reactive Cys89 on Elongin B. It showed time- and concentration-dependent labeling, with a kinact/KI of 0.30 M–1 s–1, and does not affect binding at the HIF-1α site. This hit ligand was optimized to afford compound 15 which showed improved potency and labeling of VHL. An X-ray structure of a close analogue was determined revealing the compound binding in a shallow groove on the surface of VHL. These are the first small molecules that bind covalently to an allosteric site on VHL and provide a suitable starting point for further optimization.
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Mar 2025
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Ross P.
Hryczanek
,
Andrew S.
Hackett
,
Paul
Rowland
,
Chun-Wa
Chung
,
Máire A.
Convery
,
Duncan S.
Holmes
,
Jonathan P.
Hutchinson
,
Semra
Kitchen
,
Justyna
Korczynska
,
Robert P.
Law
,
Jonathan D.
Lea
,
John
Liddle
,
Richard
Lonsdale
,
Margarete
Neu
,
Leng
Nickels
,
Alex
Phillipou
,
James E.
Rowedder
,
Jessica L.
Schneck
,
Paul
Scott-Stevens
,
Hester
Sheehan
,
Chloe L.
Tayler
,
Ioannis
Temponeras
,
Christopher P.
Tinworth
,
Ann L.
Walker
,
Justyna
Wojno-Picon
,
Robert J.
Young
,
David M.
Lindsay
,
Efstratios
Stratikos
Diamond Proposal Number(s):
[20024]
Open Access
Abstract: Endoplasmic reticulum aminopeptidase 1 (ERAP1) cleaves the N-terminal amino acids of peptides, which can then bind onto major histocompatibility class I (MHC-I) molecules for presentation onto the cell surface, driving the activation of adaptive immune responses. In cancer, overtrimming of mature antigenic peptides can reduce cytotoxic T-cell responses, and ERAP1 can generate self-antigenic peptides which contribute to autoimmune cellular responses. Therefore, modulation of ERAP1 activity has potential therapeutic indications for cancer immunotherapy and in autoimmune disease. Herein we describe the hit-to-lead optimization of a series of cyclohexyl acid ERAP1 inhibitors, found by X-ray crystallography to bind at an allosteric regulatory site. Structure-based drug design enabled a >1,000-fold increase in ERAP1 enzymatic and cellular activity, resulting in potent and selective tool molecules. For lead compound 7, rat pharmacokinetic properties showed moderate unbound clearance and oral bioavailability, thus highlighting the promise of the series for further optimization.
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Dec 2024
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[25108]
Open Access
Abstract: In this Letter, we present a small series of novel bacterial topoisomerase inhibitors (NTBIs) that exhibit both potent inhibition of Mycobacterium tuberculosis DNA gyrase and potent antimycobacterial activity. The disclosed crystal structure of M. tuberculosis DNA gyrase in complex with DNA and compound 5 from this NBTI series reveals the binding mode of an NBTI in the GyrA binding pocket and confirms the presence and importance of halogen bonding for the excellent on-target potency. In addition, we have shown that compound 5 is a promising M. tuberculosis DNA gyrase inhibitor, with an IC50 for M. tuberculosis gyrase of 0.096 μM, and it has potent activity against M. tuberculosis, with an IC50 of 0.165 μM.
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Nov 2024
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I04-Macromolecular Crystallography
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Frances M.
Bashore
,
Sophia M.
Min
,
Xiangrong
Chen
,
Stefanie
Howell
,
Caroline H.
Rinderle
,
Gabriel
Morel
,
Josie A.
Silvaroli
,
Carrow I.
Wells
,
Bruce A.
Bunnell
,
David H.
Drewry
,
Navjot S.
Pabla
,
Sila K.
Ultanir
,
Alex N.
Bullock
,
Alison D.
Axtman
Open Access
Abstract: Acylaminoindazole-based inhibitors of CDKL2 were identified via analyses of cell-free binding and selectivity data. Compound 9 was selected as a CDKL2 chemical probe based on its potent inhibition of CDKL2 enzymatic activity, engagement of CDKL2 in cells, and excellent kinome-wide selectivity, especially when used in cells. Compound 16 was designed as a negative control to be used alongside compound 9 in experiments to interrogate CDKL2-mediated biology. A solved cocrystal structure of compound 9 bound to CDKL2 highlighted key interactions it makes within its ATP-binding site. Inhibition of downstream phosphorylation of EB2, a CDKL2 substrate, in rat primary neurons provided evidence that engagement of CDKL2 by compound 9 in cells resulted in inhibition of its activity. When used at relevant concentrations, compound 9 does not impact the viability of rat primary neurons or certain breast cancer cells nor elicit consistent changes in the expression of proteins involved in epithelial–mesenchymal transition.
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Aug 2024
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I24-Microfocus Macromolecular Crystallography
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Open Access
Abstract: Galectin-8 contains two different carbohydrate recognition domains (CRDs). Selective inhibitors for at least one CRD are desirable for galectin-8 biology studies and potentially for pharmacological purposes. Structure-guided design led to the discovery of potent and selective glycomimetic–heterocycle hybrid ligands, with a 4-(p-bromophenyl)phthalazinone derivative displaying a 34 μM Kd for galectin-8N (N-terminal CRD), no binding to galectin-8C (C-terminal CRD), -1, -3, -4N, -7, -9C, or -9N, and >40-fold selectivity over galectin-4C. Selectivity was achieved with the halogenated 4-phenylphthalazinone moiety occupying a galectin-8N-specific sub-pocket. A 1.30 Å resolution X-ray structure revealed the phthalazinone moiety stacking with Arg45 and the 4-bromophenyl moiety stacking both Arg59 and Tyr141 of galectin-8N. Physicochemical and in vitro ADME studies revealed a desirable LogD, which also translated to good passive permeability. The chemical, microsome, and plasma stability support these compounds as promising tool compounds and candidates for hit-to-lead optimization.
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Aug 2024
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Gavin W.
Collie
,
Ulf
Börjesson
,
Yunhua
Chen
,
Zhiqiang
Dong
,
Paolo
Di Fruscia
,
Andrea
Gohlke
,
Anna
Hoyle
,
Thomas A.
Hunt
,
Mehul H.
Jesani
,
Haiou
Luo
,
Jakub
Luptak
,
Alexander G.
Milbradt
,
Priyanka
Narasimhan
,
Martin
Packer
,
Saleha
Patel
,
Jingchuan
Qiao
,
R. Ian
Storer
,
Christopher J.
Stubbs
,
Jonathan
Tart
,
Caroline
Truman
,
Anderson T.
Wang
,
Matthew G.
Wheeler
,
Jon
Winter-Holt
Diamond Proposal Number(s):
[20015]
Open Access
Abstract: MUS81 is a structure-selective endonuclease that cleaves various branched DNA structures arising from natural physiological processes such as homologous recombination and mitosis. Due to this, MUS81 is able to relieve replication stress, and its function has been reported to be critical to the survival of many cancers, particularly those with dysfunctional DNA-repair machinery. There is therefore interest in MUS81 as a cancer drug target, yet there are currently few small molecule inhibitors of this enzyme reported, and no liganded crystal structures are available to guide hit optimization. Here we report the fragment-based discovery of novel small molecule MUS81 inhibitors with sub-μM biochemical activity. These inhibitors were used to develop a novel crystal system, providing the first structural insight into the inhibition of MUS81 with small molecules.
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Jun 2024
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I04-Macromolecular Crystallography
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Simon C. C.
Lucas
,
J. Henry
Blackwell
,
Ulf
Börjesson
,
David
Hargreaves
,
Alexander G.
Milbradt
,
Samiyah
Ahmed
,
Mark J.
Bostock
,
Carine
Guerot
,
Andrea
Gohlke
,
Olaf
Kinzel
,
Michelle L.
Lamb
,
Nidhal
Selmi
,
Christopher J.
Stubbs
,
Nancy
Su
,
Qibin
Su
,
Haiou
Luo
,
Ting
Xiong
,
Xiaoqian
Zuo
,
Sana
Bazzaz
,
Corey
Bienstock
,
Paolo A.
Centrella
,
Kyle E.
Denton
,
Diana
Gikunju
,
Marie-Aude
Guié
,
John P.
Guilinger
,
Christopher
Hupp
,
Anthony D.
Keefe
,
Takashi
Satoh
,
Ying
Zhang
,
Emma L.
Rivers
Abstract: Bfl-1 is overexpressed in both hematological and solid tumors; therefore, inhibitors of Bfl-1 are highly desirable. A DNA-encoded chemical library (DEL) screen against Bfl-1 identified the first known reversible covalent small-molecule ligand for Bfl-1. The binding was validated through biophysical and biochemical techniques, which confirmed the reversible covalent mechanism of action and pointed to binding through Cys55. This represented the first identification of a cyano-acrylamide reversible covalent compound from a DEL screen and highlights further opportunities for covalent drug discovery through DEL screening. A 10-fold improvement in potency was achieved through a systematic SAR exploration of the hit. The more potent analogue compound 13 was successfully cocrystallized in Bfl-1, revealing the binding mode and providing further evidence of a covalent interaction with Cys55.
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Jun 2024
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